9DOV image
Deposition Date 2024-09-19
Release Date 2026-05-20
Last Version Date 2026-05-20
Entry Detail
PDB ID:
9DOV
Keywords:
RIBOSOME
Title:
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B
Biological Source:
Source Organism(s):
Taura syndrome virus (Taxon ID: 142102)
Saccharomyces cerevisiae (Taxon ID: 4932)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.49 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9DOV validation report missing
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:LA (auth: A1)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:MA (auth: A3)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:NA (auth: A4)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:IA (auth: AA)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX45 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:JA (auth: AB)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14126 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:KA (auth: AC)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P10664 Pfam ID:PF00573, PF14374
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL5
Chain IDs:OA (auth: AD)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26321 Pfam ID:PF17144, PF14204
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:PA (auth: AE)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02326 Pfam ID:PF01159
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:QA (auth: AF)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05737 Pfam ID:PF08079, PF00327
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:RA (auth: AG)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P17076 Pfam ID:PF01248
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:SA (auth: AH)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05738 Pfam ID:PF00347
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL10
Chain IDs:TA (auth: AI)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41805 Pfam ID:PF00252
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL11A
Chain IDs:UA (auth: AJ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0W9 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:VA (auth: AL)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12690 Pfam ID:PF01294
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:WA (auth: AM)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36105 Pfam ID:PF00467, PF01929
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:XA (auth: AN)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05748 Pfam ID:PF00827
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:YA (auth: AO)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26784 Pfam ID:PF00572
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:ZA (auth: AP)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05740 Pfam ID:PF00237
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:AB (auth: AQ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX49 Pfam ID:PF17135
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:BB (auth: AR)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX82 Pfam ID:PF01280, PF25476
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20
Gene (Uniprot):SCRG_02137
Chain IDs:CB (auth: AS)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:B3LMD0
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:DB (auth: AT)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02753 Pfam ID:PF01157
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:EB (auth: AU)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05749 Pfam ID:PF01776
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:FB (auth: AV)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX41 Pfam ID:PF00238
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL24A
Chain IDs:GB (auth: AW)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04449 Pfam ID:PF01246
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:HB (auth: AX)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04456 Pfam ID:PF03939, PF00276
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:IB (auth: AY)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:JB (auth: AZ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H6 Pfam ID:PF01777
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:KB (auth: Aa)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P02406 Pfam ID:PF00828
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL29
Chain IDs:LB (auth: Ab)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05747 Pfam ID:PF01779
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:MB (auth: Ac)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14120 Pfam ID:PF01248
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:NB (auth: Ad)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H8 Pfam ID:PF01198
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL32
Chain IDs:OB (auth: Ae)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38061 Pfam ID:PF01655
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:PB (auth: Af)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05744 Pfam ID:PF01247
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:QB (auth: Ag)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P87262 Pfam ID:PF01199
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:RB (auth: Ah)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX84 Pfam ID:PF00831
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:SB (auth: Ai)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05745 Pfam ID:PF01158
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:TB (auth: Aj)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49166 Pfam ID:PF01907
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL38
Chain IDs:UB (auth: Ak)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49167 Pfam ID:PF01781
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:VB (auth: Al)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04650 Pfam ID:PF00832
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal prote
Gene (Uniprot):RPL40A
Chain IDs:WB (auth: Am)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CH08 Pfam ID:PF00240, PF01020
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41-A
Gene (Uniprot):RPL41A
Chain IDs:XB (auth: An)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX86 Pfam ID:PF05162
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Gene (Uniprot):RPL42A
Chain IDs:YB (auth: Ao)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX27 Pfam ID:PF00935
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:ZB (auth: Ap)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX25 Pfam ID:PF01780
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:HA (auth: B5)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S0-A
Gene (Uniprot):RPS0A
Chain IDs:A (auth: BA)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32905 Pfam ID:PF00318
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS1A
Chain IDs:B (auth: BB)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:B3RHV0,P33442 Pfam ID:PF01015
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS2
Chain IDs:C (auth: BC)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25443 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS3
Chain IDs:S (auth: BD)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05750 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4-A
Gene (Uniprot):RPS4A
Chain IDs:D (auth: BE)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX35 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Rps5p
Gene (Uniprot):RPS5
Chain IDs:T (auth: BF)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:A0A1L4AA68
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6-A
Gene (Uniprot):RPS6A
Chain IDs:E (auth: BG)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX37 Pfam ID:PF01092
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7-A
Gene (Uniprot):RPS7A
Chain IDs:F (auth: BH)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26786 Pfam ID:PF01251
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8-A
Gene (Uniprot):RPS8A
Chain IDs:G (auth: BI)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX39 Pfam ID:PF01201
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:H (auth: BJ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:O13516 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10-A
Gene (Uniprot):RPS10A
Chain IDs:U (auth: BK)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q08745 Pfam ID:PF03501
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-A
Gene (Uniprot):RPS11A
Chain IDs:I (auth: BL)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX47 Pfam ID:PF16205, PF00366
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS12
Chain IDs:GA (auth: BM)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P48589 Pfam ID:PF01248
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:J (auth: BN)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05756 Pfam ID:PF08069, PF00312
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-A
Gene (Uniprot):RPS14A
Chain IDs:K (auth: BO)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P06367 Pfam ID:PF00411
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS15
Chain IDs:V (auth: BP)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q01855 Pfam ID:PF00203
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-A
Gene (Uniprot):RPS16A
Chain IDs:W (auth: BQ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX51 Pfam ID:PF00380
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17-A
Gene (Uniprot):RPS17A
Chain IDs:X (auth: BR)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P02407 Pfam ID:PF00833
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18-A
Gene (Uniprot):RPS18A
Chain IDs:Y (auth: BS)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX55 Pfam ID:PF00416
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19-A
Gene (Uniprot):RPS19A
Chain IDs:Z (auth: BT)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P07280 Pfam ID:PF01090
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS20
Chain IDs:AA (auth: BU)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38701 Pfam ID:PF00338
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21-A
Gene (Uniprot):RPS21A
Chain IDs:L (auth: BV)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0V8 Pfam ID:PF01249
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS22A
Chain IDs:M (auth: BW)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0W1 Pfam ID:PF00410
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23-A
Gene (Uniprot):RPS23A
Chain IDs:N (auth: BX)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX29 Pfam ID:PF00164
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24-A
Gene (Uniprot):RPS24A
Chain IDs:O (auth: BY)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX31 Pfam ID:PF01282
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS25A
Chain IDs:BA (auth: BZ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q3E792 Pfam ID:PF03297
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS26B
Chain IDs:P (auth: Ba)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P39939 Pfam ID:PF01283
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27-A
Gene (Uniprot):RPS27A
Chain IDs:Q (auth: Bb)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P35997 Pfam ID:PF01667
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS28A
Chain IDs:CA (auth: Bc)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q3E7X9 Pfam ID:PF01200
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPS29A
Chain IDs:DA (auth: Bd)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41057 Pfam ID:PF00253
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30-A
Gene (Uniprot):RPS30A
Chain IDs:R (auth: Be)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX33 Pfam ID:PF04758
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:RPS31 isoform 1
Gene (Uniprot):RPS31
Chain IDs:FA (auth: Bf)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:A0ABF7PIT7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding pr
Gene (Uniprot):ASC1
Chain IDs:EA (auth: Bg)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38011 Pfam ID:PF00400
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL1A
Chain IDs:AC (auth: E)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX43 Pfam ID:PF00687
Polymer Type:polyribonucleotide
Molecule:TSV IRES RNA
Chain IDs:BC (auth: EC)
Chain Length:0
Number of Molecules:1
Biological Source:Taura syndrome virus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
4AC HA C modified residue
A2M HA A modified residue
G7M HA G modified residue
HIC JA HIS modified residue
MA6 HA A modified residue
OMC HA C modified residue
OMG HA G modified residue
OMU HA U modified residue
XSX HA U modified residue
Ligand Molecules
HYG
MG
ZN
Primary Citation
Structural basis for hygromycin B inhibition of yeast pseudouridine-deficient ribosomes.
Sci Adv 11 eadu0151 eadu0151 (2025)
PMID: 40173234 DOI: 10.1126/sciadv.adu0151

Abstact

Eukaryotic ribosomes are enriched with pseudouridine, particularly at the functional centers targeted by antibiotics. Here, we investigated the roles of pseudouridine in aminoglycoside-mediated translation inhibition by comparing the structural and functional properties of the yeast wild-type and the pseudouridine-free ribosomes. We showed that the pseudouridine-free ribosomes have decreased thermostability and high sensitivity to aminoglycosides. When presented with a model internal ribosomal entry site RNA, elongation factor eEF2, GTP (guanosine triphosphate), and sordarin, hygromycin B preferentially binds to the pseudouridine-free ribosomes during initiation by blocking eEF2 binding, stalling ribosomes in a nonrotated conformation. The structures captured hygromycin B bound at the intersubunit bridge B2a enriched with pseudouridine and a deformed codon-anticodon duplex, revealing a functional link between pseudouridine and aminoglycoside inhibition. Our results suggest that pseudouridine enhances both thermostability and conformational fitness of the ribosomes, thereby influencing their susceptibility to aminoglycosides.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
9DOV
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