9YWB image
Deposition Date 2025-10-24
Release Date 2026-11-04
Last Version Date 2026-11-04
Entry Detail
PDB ID:
9YWB
Keywords:
RIBOSOME
Title:
Hypomethylated nucleoplasmic pre-60S intermediate containing Nog2 at Rsa4-arrested 5S post-rotation state
Biological Source:
Source Organism(s):
Saccharomyces cerevisiae BY4741 (Taxon ID: 1247190)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.85 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9YWB validation report missing
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S ribosomal RNA
Chain IDs:RA (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:WA (auth: 2)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:SA (auth: 3)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable metalloprotease ARX1
Gene (Uniprot):ARX1
Chain IDs:ZA (auth: 4)
Chain Length:593
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q03862 EC:3.-.-.-
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein CGR1
Gene (Uniprot):CGR1
Chain IDs:TA (auth: 5)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P53188
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:C (auth: A)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX45
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:E (auth: B)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P14126
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:G (auth: C)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P10664
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:A (auth: D)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P26321
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:J (auth: E)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q02326
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:L (auth: F)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05737
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL8A
Chain IDs:N (auth: G)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P17076
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL9A
Chain IDs:Q (auth: H)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05738
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bud site selection protein 20
Gene (Uniprot):BUD20
Chain IDs:P (auth: I)
Chain Length:166
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q08004
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11-A
Gene (Uniprot):RPL11A
Chain IDs:B (auth: J)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0C0W9
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12
Chain IDs:QA (auth: K)
Chain Length:165
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:V (auth: L)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q12690
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):RPL41A
Chain IDs:DB (auth: Lr)
Chain Length:25
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX86
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:X (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P36105
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL15A
Chain IDs:Z (auth: N)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05748
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL16A
Chain IDs:BA (auth: O)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P26784
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:CA (auth: P)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05740
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:DA (auth: Q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX49
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:EA (auth: R)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX82
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL20A
Chain IDs:GA (auth: S)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX23
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:HA (auth: T)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q02753
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:IA (auth: U)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05749
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:JA (auth: V)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX41
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome assembly factor MRT4
Gene (Uniprot):MRT4
Chain IDs:KA (auth: W)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P33201
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:LA (auth: X)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P04456
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:MA (auth: Y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05743
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:OA (auth: Z)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0C2H6
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:D (auth: a)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P02406
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein
Gene (Uniprot):NOG1
Chain IDs:F (auth: b)
Chain Length:647
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q02892
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:H (auth: c)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P14120
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:I (auth: d)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0C2H8
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:K (auth: e)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P38061
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:M (auth: f)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05744
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:O (auth: g)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P87262
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:R (auth: h)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX84
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:S (auth: i)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05745
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:T (auth: j)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P49166
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:U (auth: k)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P49167
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:W (auth: l)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P04650
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein
Gene (Uniprot):NOG2
Chain IDs:VA (auth: m)
Chain Length:486
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P53742
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-rRNA-processing protein I
Gene (Uniprot):IPI1
Chain IDs:YA (auth: n)
Chain Length:334
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:A6ZSZ4
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein A
Gene (Uniprot):ALB1
Chain IDs:AB (auth: o)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:A6ZQK9
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:Y (auth: p)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX25
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nuclear GTP-binding protein N
Gene (Uniprot):NUG1
Chain IDs:CB (auth: q)
Chain Length:520
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P40010
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein N
Gene (Uniprot):NSA2
Chain IDs:FA (auth: r)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P40078
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):RPL1A
Chain IDs:BB (auth: s)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX43
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein SDA1
Gene (Uniprot):SDA1
Chain IDs:XA (auth: t)
Chain Length:767
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P53313
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein R
Gene (Uniprot):RLP24
Chain IDs:AA (auth: u)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q07915
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome assembly protein 4
Gene (Uniprot):RSA4
Chain IDs:UA (auth: x)
Chain Length:515
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P25382
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initia
Gene (Uniprot):TIF6
Chain IDs:NA (auth: y)
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q12522
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:UPF0642 protein YBL028C
Gene (Uniprot):YBL0423
Chain IDs:PA (auth: z)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P38202
Ligand Molecules
GTP
K
MG
Primary Citation
2'-O-methylation regulates ribosome biogenesis
To Be Published ? ? ? (?)
Primary Citation of related structures
9YWB
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