ISDA: 9H6I

Deposition Date 2024-10-24

Release Date 2026-02-04

Last Version Date 2026-06-24

Entry Detail

PDB ID:

9H6I

Keywords:

RIBOSOME

Title:

Structure of the Arabidopsis thaliana 80S ribosome in complex with P- and E-site tRNAs, mRNA, and thermospermine

Biological Source:

Source Organism(s):

Arabidopsis thaliana (Taxon ID: 3702)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.20 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:Transfer RNA Phe (GAA)
Chain IDs:A (auth: 2), YB (auth: W2)
Chain Length:76
Number of Molecules:2
Biological Source:Arabidopsis thaliana

Polymer Type:polyribonucleotide
Molecule:Ribosomal RNA 5.8S
Chain IDs:B (auth: 3)
Chain Length:164
Number of Molecules:1
Biological Source:Arabidopsis thaliana

Polymer Type:polyribonucleotide
Molecule:Ribosomal RNA 25S
Chain IDs:C (auth: A)
Chain Length:3385
Number of Molecules:1
Biological Source:Arabidopsis thaliana

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS3A
Chain IDs:AB (auth: AA)
Chain Length:250
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9SIP7 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS9C
Chain IDs:YA (auth: AB)
Chain Length:197
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9FLF0 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS2B, US5U, US5V
Chain IDs:X (auth: AC)
Chain Length:284
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q93VB8 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS5B
Chain IDs:CA (auth: AD)
Chain Length:207
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P51427 Pfam ID:PF00177

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS15AA, RPS15AF
Chain IDs:L (auth: AE)
Chain Length:130
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P42798 Pfam ID:PF00410

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS16A
Chain IDs:EB (auth: AF)
Chain Length:146
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9SK22 Pfam ID:PF00380

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL13B
Chain IDs:BB (auth: AG)
Chain Length:206
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P41127 Pfam ID:PF01294

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL14B
Chain IDs:Z (auth: AH)
Chain Length:134
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9T043 Pfam ID:PF01929

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS10A
Chain IDs:AC (auth: AI)
Chain Length:177
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9SW09 Pfam ID:PF03501

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL18C
Chain IDs:DA (auth: AJ)
Chain Length:187
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q940B0 Pfam ID:PF17135

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL19A
Chain IDs:WA (auth: AK)
Chain Length:214
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9SRX2 Pfam ID:PF01280, PF25476

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L18ae/LX fa
Gene (Uniprot):L18AB
Chain IDs:Q (auth: AL)
Chain Length:217
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:A0A1P8AY36 Pfam ID:PF01775

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL21A, RPL21C
Chain IDs:W (auth: AM)
Chain Length:164
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q43291 Pfam ID:PF01157

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL22B
Chain IDs:PB (auth: AN)
Chain Length:124
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9M9W1 Pfam ID:PF01776

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL24A
Chain IDs:UA (auth: AO)
Chain Length:164
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q42347 Pfam ID:PF01246

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL27C
Chain IDs:N (auth: AP)
Chain Length:135
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P51419 Pfam ID:PF01777

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL28A
Chain IDs:KB (auth: AQ)
Chain Length:143
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:O82204 Pfam ID:PF01778

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):T8E24.9
Chain IDs:H (auth: AR)
Chain Length:83
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:F4JC32 Pfam ID:PF01779

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL30B
Chain IDs:IA (auth: AT)
Chain Length:112
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q8VZ19 Pfam ID:PF01248

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL31B
Chain IDs:I (auth: AU)
Chain Length:119
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9STR1 Pfam ID:PF01198

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL32A
Chain IDs:BA (auth: AV)
Chain Length:133
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P49211 Pfam ID:PF01655

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL35AC
Chain IDs:T (auth: AW)
Chain Length:112
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9C912 Pfam ID:PF01247

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL36B
Chain IDs:M (auth: AX)
Chain Length:112
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9M352 Pfam ID:PF01158

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL37A
Chain IDs:UB (auth: AY)
Chain Length:95
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q8LFH7 Pfam ID:PF01907

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL38A, RPL38B
Chain IDs:HB (auth: AZ)
Chain Length:69
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:O22860 Pfam ID:PF01781

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS8A
Chain IDs:TB (auth: Aa)
Chain Length:222
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q93VG5 Pfam ID:PF01201

Polymer Type:polyribonucleotide
Molecule:Messenger RNA (poly-U)
Chain IDs:XB (auth: B1)
Chain Length:12
Number of Molecules:1
Biological Source:Arabidopsis thaliana

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL39A, RPL39C
Chain IDs:DB (auth: BA)
Chain Length:51
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P51424 Pfam ID:PF00832

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS17D
Chain IDs:OB (auth: BB)
Chain Length:141
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9LZ17 Pfam ID:PF00833

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPL41A, RPL41C, RPL41D, RPL41E, RPL41G
Chain IDs:E (auth: BC)
Chain Length:25
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P62120 Pfam ID:PF05162

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL36AA, RPL36AB
Chain IDs:U (auth: BD)
Chain Length:105
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:O23290 Pfam ID:PF00935

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL37AC
Chain IDs:IB (auth: BE)
Chain Length:92
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q8RXU5 Pfam ID:PF01780

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL6B
Chain IDs:ZA (auth: BF)
Chain Length:233
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9C9C6 Pfam ID:PF03868, PF01159

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL7AB
Chain IDs:MA (auth: BG)
Chain Length:256
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9LZH9 Pfam ID:PF01248

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL13AB
Chain IDs:FA (auth: BH)
Chain Length:206
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9LRX8 Pfam ID:PF00572

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL23A, RPL23B, RPL23C
Chain IDs:Y (auth: BI)
Chain Length:140
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P49690 Pfam ID:PF00238

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL10B
Chain IDs:TA (auth: BJ)
Chain Length:221
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q08770 Pfam ID:PF00252

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL5A
Chain IDs:HA (auth: BK)
Chain Length:301
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q8LBI1 Pfam ID:PF17144, PF14204

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS19C
Chain IDs:RB (auth: BL)
Chain Length:143
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9FNP8 Pfam ID:PF01090

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL17A
Chain IDs:F (auth: BM)
Chain Length:176
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q93VI3 Pfam ID:PF00237

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL23AB
Chain IDs:LA (auth: BN)
Chain Length:154
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9M3C3 Pfam ID:PF03939, PF00276

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL26A
Chain IDs:G (auth: BO)
Chain Length:146
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P51414 Pfam ID:PF16906, PF00467

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL35C
Chain IDs:KA (auth: BP)
Chain Length:123
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9M3D2 Pfam ID:PF00831

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL8A
Chain IDs:EA (auth: BQ)
Chain Length:258
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P46286 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L30/L7 fami
Gene (Uniprot):F6E13.25
Chain IDs:QA (auth: BR)
Chain Length:247
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:F4IT48 Pfam ID:PF08079, PF00327

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):ARP1
Chain IDs:V (auth: BS)
Chain Length:389
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P17094 Pfam ID:PF00297

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL4A
Chain IDs:AA (auth: BT)
Chain Length:406
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9SF40 Pfam ID:PF00573, PF14374

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL11A
Chain IDs:PA (auth: BU)
Chain Length:182
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P42795 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS3AB
Chain IDs:SA (auth: BV)
Chain Length:262
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q42262 Pfam ID:PF01015

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS21C
Chain IDs:VA (auth: BW)
Chain Length:82
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q3E902 Pfam ID:PF01249

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS20B
Chain IDs:ZB (auth: Ba)
Chain Length:122
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9STY6 Pfam ID:PF00338

Polymer Type:polyribonucleotide
Molecule:Ribosomal RNA 5S
Chain IDs:D (auth: C3)
Chain Length:121
Number of Molecules:1
Biological Source:Arabidopsis thaliana

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS29A, RPS29B, RPS29C
Chain IDs:VB (auth: Ca)
Chain Length:56
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q680P8 Pfam ID:PF00253

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS13B
Chain IDs:GA (auth: Da)
Chain Length:151
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P59224 Pfam ID:PF08069, PF00312

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL15A
Chain IDs:P (auth: Ea)
Chain Length:204
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:O23515 Pfam ID:PF00827

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL34A
Chain IDs:NA (auth: Fa)
Chain Length:120
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q42351 Pfam ID:PF01199

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-ribosomal protein e
Gene (Uniprot):RPL40A
Chain IDs:CB (auth: Ga)
Chain Length:128
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:B9DHA6 Pfam ID:PF00240, PF01020

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL27AC
Chain IDs:OA (auth: Ha)
Chain Length:146
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P49637 Pfam ID:PF00828

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL9B, RPL9C
Chain IDs:K (auth: Ia)
Chain Length:194
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P49209 Pfam ID:PF00347

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS4D
Chain IDs:O (auth: Ja)
Chain Length:262
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q8VYK6 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS24B
Chain IDs:S (auth: Ka)
Chain Length:133
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q8LC83 Pfam ID:PF01282

Polymer Type:polypeptide(L)
Molecule:Nascent polypeptide
Chain IDs:BC (auth: L3)
Chain Length:23
Number of Molecules:1
Biological Source:Arabidopsis thaliana

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS25E
Chain IDs:SB (auth: La)
Chain Length:108
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9T029 Pfam ID:PF03297

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS26A
Chain IDs:J (auth: Ma)
Chain Length:131
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P49206 Pfam ID:PF01283

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS27B
Chain IDs:XA (auth: Na)
Chain Length:86
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9M2F1 Pfam ID:PF01667

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS28C
Chain IDs:LB (auth: Oa)
Chain Length:64
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P34789 Pfam ID:PF01200

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS30A, RPS30B, RPS30C
Chain IDs:JA (auth: Pa)
Chain Length:62
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P49689 Pfam ID:PF04758

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS7C
Chain IDs:QB (auth: Ra)
Chain Length:190
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q8LD03 Pfam ID:PF01251

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS6B
Chain IDs:GB (auth: Ta)
Chain Length:249
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P51430 Pfam ID:PF01092

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS14B
Chain IDs:MB (auth: Ua)
Chain Length:150
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9CAX6 Pfam ID:PF00411

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS23B
Chain IDs:R (auth: Va)
Chain Length:142
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P49201 Pfam ID:PF00164

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS18A, RPS18B, RPS18C
Chain IDs:FB (auth: Wa)
Chain Length:152
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P34788 Pfam ID:PF00416

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS11A
Chain IDs:RA (auth: Xa)
Chain Length:160
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P16181 Pfam ID:PF16205, PF00366

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS15C
Chain IDs:NB (auth: Ya)
Chain Length:150
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q9FY65 Pfam ID:PF00203

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPSaA
Chain IDs:JB (auth: Za)
Chain Length:298
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q08682 Pfam ID:PF00318

Polymer Type:polyribonucleotide
Molecule:Ribosomal RNA 18S
Chain IDs:WB (auth: h1)
Chain Length:1805
Number of Molecules:1
Biological Source:Arabidopsis thaliana

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
A2M	B	A	modified residue
HIC	V	HIS	modified residue
MLY	CB	LYS	modified residue
OMG	B	G	modified residue
PSU	B	U	modified residue

Ligand Molecules

EPE

SPD

TER

Primary Citation

Recruitment of bifunctional regulator thermospermine to methylated ribosomes directs xylem fate.

Ko, D, Ruonala, R, Faille, A, Hellmann, E, Help, H, Liu, H, Nielsen, R, Haakonsson, A, De Diego, N, Paatero, A, Shcherbii, M.V, Stefanowicz, K, Cavar Zeljkovic, S, Drud Lundager Rasmussen, T, Novak, O, Bodi, Z, Eswaran, G, Wybouw, B, Bourdon, M, Urbez, C, Liu, X, Salokas, K, Ohman, T, Waldie, T, Toronen, P, El-Showk, S, Balcerowicz, M, Besnard, F, Liu, X, Perkins, P, Mazzoni-Putman, S, Vainonen, J.P, Sierla, M, Frilander, M.J, Mandrup, S, Vernoux, T, Ljung, K, Ferrando, A, Blazquez, M.A, Holm, L, Fray, R, Varjosalo, M, Leyser, O, Paavilainen, V.O, Mahonen, A.P, Stepanova, A, Alonso, J, Heber, S, Malinowski, R, Kirpekar, F, Warren, A.J, Helariutta, Y.Show

Science 391 694 699 (2026)

PMID: 41678627 DOI: 10.1126/science.adx2867

Abstact

Polyamines are often associated with ribosomes and are thought to stabilize their integrity. In Arabidopsis, the polyamine thermospermine (tSpm) affects xylem cell fate. tSpm induces translation of SUPPRESSOR-OF-ACAULIS51 (SAC51) and SAC51-LIKEs (SACLs), which inhibit heterodimerization of the xylem development proteins LONESOME-HIGHWAY (LHW) and TARGET-OF-MONOPTEROS5. Here, we report a methyltransferase, OVERACHIEVER, that methylates the peptidyl transferase center of the 25S ribosomal RNA (rRNA). Residue m(3)U2952 promotes functional tSpm binding to a specific site connecting the P-site transfer RNA (tRNA) with rRNA residues in the peptidyl transferase center. This interaction enhances the translation of SACLs but inhibits that of LHW. Our study uncovers the dependency between a conserved rRNA base methylation and a polyamine in orchestrating cell fate decisions, highlighting a role for the ribosome chemical landscape in translational regulation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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