9YWB | pdb_00009ywb

Hypomethylated nucleoplasmic pre-60S intermediate containing Nog2 at Rsa4-arrested 5S post-rotation state

PDB DOI: https://doi.org/10.2210/pdb9YWB/pdb
EM Map EMD-73543: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Saccharomyces cerevisiae BY4741
Mutation(s): No

Deposited: 2025-10-24 Released: 2026-11-04
Deposition Author(s): Zhao, Y., Li, H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.85 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

2'-O-methylation regulates ribosome biogenesis

Zhao, Y., Li, H.

To be published.

Macromolecule Content

Total Structure Weight: 2,502.35 kDa
Atom Count: 148,851
Modeled Residue Count: 13,034
Deposited Residue Count: 15,341
Unique protein chains: 53
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L5	A [auth D]	297	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26321 Go to UniProtKB: P26321
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26321
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L11-A	B [auth J]	174	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C0W9 Go to UniProtKB: P0C0W9
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C0W9
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L2-A	C [auth A]	254	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX45 Go to UniProtKB: P0CX45
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CX45
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L28	D [auth a]	149	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02406 Go to UniProtKB: P02406
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02406
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L3	E [auth B]	387	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14126 Go to UniProtKB: P14126
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14126
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleolar GTP-binding protein 1	F [auth b]	647	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for Q02892 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02892 Go to UniProtKB: Q02892
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02892
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L4-A	G [auth C]	362	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P10664 Go to UniProtKB: P10664
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10664
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L30	H [auth c]	105	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14120 Go to UniProtKB: P14120
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14120
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L31-A	I [auth d]	113	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C2H8 Go to UniProtKB: P0C2H8
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C2H8
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L6-A	J [auth E]	176	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02326 Go to UniProtKB: Q02326
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02326
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L32	K [auth e]	130	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38061 Go to UniProtKB: P38061
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38061
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7-A	L [auth F]	244	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05737 Go to UniProtKB: P05737
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05737
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L33-A	M [auth f]	107	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05744 Go to UniProtKB: P05744
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05744
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL8A	N [auth G]	256	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P17076 Go to UniProtKB: P17076
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17076
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L34-A	O [auth g]	121	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P87262 Go to UniProtKB: P87262
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P87262
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Bud site selection protein 20	P [auth I]	166	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for Q08004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08004 Go to UniProtKB: Q08004
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08004
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL6A	Q [auth H]	191	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05738 Go to UniProtKB: P05738
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05738
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35-A	R [auth h]	120	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX84 Go to UniProtKB: P0CX84
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CX84
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L36-A	S [auth i]	100	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05745 Go to UniProtKB: P05745
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05745
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L37-A	T [auth j]	88	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49166 Go to UniProtKB: P49166
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49166
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L38	U [auth k]	78	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49167 Go to UniProtKB: P49167
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49167
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13-A	V [auth L]	199	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12690 Go to UniProtKB: Q12690
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UniProt Group	Q12690
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L39	W [auth l]	51	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04650 Go to UniProtKB: P04650
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04650
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L14-A	X [auth M]	138	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36105 Go to UniProtKB: P36105
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UniProt Group	P36105
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L43-A	Y [auth p]	92	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX25 Go to UniProtKB: P0CX25
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CX25
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL15A	Z [auth N]	204	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05748 Go to UniProtKB: P05748
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05748
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome biogenesis protein RLP24	AA [auth u]	199	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for Q07915 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q07915 Go to UniProtKB: Q07915
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07915
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL13A	BA [auth O]	199	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26784 Go to UniProtKB: P26784
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26784
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L17-A	CA [auth P]	184	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05740 Go to UniProtKB: P05740
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05740
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18-A	DA [auth Q]	186	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX49 Go to UniProtKB: P0CX49
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CX49
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L19-A	EA [auth R]	189	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX82 Go to UniProtKB: P0CX82
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CX82
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome biogenesis protein NSA2	FA [auth r]	261	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P40078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40078 Go to UniProtKB: P40078
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UniProt Group	P40078
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL20A	GA [auth S]	172	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX23 Go to UniProtKB: P0CX23
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CX23
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L21-A	HA [auth T]	160	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02753 Go to UniProtKB: Q02753
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UniProt Group	Q02753
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L22-A	IA [auth U]	121	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05749 Go to UniProtKB: P05749
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05749
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23-A	JA [auth V]	137	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX41 Go to UniProtKB: P0CX41
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CX41
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome assembly factor MRT4	KA [auth W]	236	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P33201 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33201 Go to UniProtKB: P33201
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UniProt Group	P33201
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L25	LA [auth X]	142	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04456 Go to UniProtKB: P04456
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04456
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L26-A	MA [auth Y]	127	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05743 Go to UniProtKB: P05743
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05743
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 6	NA [auth y]	245	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12522 Go to UniProtKB: Q12522
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12522
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27-A	OA [auth Z]	136	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C2H6 Go to UniProtKB: P0C2H6
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UniProt Group	P0C2H6
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0642 protein YBL028C	PA [auth z]	106	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P38202 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38202 Go to UniProtKB: P38202
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UniProt Group	P38202
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L12	QA [auth K]	165	Saccharomyces cerevisiae BY4741	Mutation(s): 0
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA-processing protein CGR1	TA [auth 5]	120	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P53188 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53188 Go to UniProtKB: P53188
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UniProt Group	P53188
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome assembly protein 4	UA [auth x]	515	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P25382 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25382 Go to UniProtKB: P25382
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25382
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleolar GTP-binding protein 2	VA [auth m]	486	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P53742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53742 Go to UniProtKB: P53742
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UniProt Group	P53742
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SDA1	XA [auth t]	767	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P53313 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53313 Go to UniProtKB: P53313
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53313
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-rRNA-processing protein IPI1	YA [auth n]	334	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for A6ZSZ4 (Saccharomyces cerevisiae (strain YJM789)) Explore A6ZSZ4 Go to UniProtKB: A6ZSZ4
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UniProt Group	A6ZSZ4
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable metalloprotease ARX1	ZA [auth 4]	593	Saccharomyces cerevisiae BY4741	Mutation(s): 0 EC: 3
UniProt
Find proteins for Q03862 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03862 Go to UniProtKB: Q03862
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UniProt Group	Q03862
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Reference Sequence

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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome biogenesis protein ALB1	AB [auth o]	175	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for A6ZQK9 (Saccharomyces cerevisiae (strain YJM789)) Explore A6ZQK9 Go to UniProtKB: A6ZQK9
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UniProt Group	A6ZQK9
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL1A	BB [auth s]	217	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P0CX43 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX43 Go to UniProtKB: P0CX43
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UniProt Group	P0CX43
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear GTP-binding protein NUG1	CB [auth q]	520	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P40010 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40010 Go to UniProtKB: P40010
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UniProt Group	P40010
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Reference Sequence

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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS32A	DB [auth Lr]	25	Saccharomyces cerevisiae BY4741	Mutation(s): 0
UniProt
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX86 Go to UniProtKB: P0CX86
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UniProt Group	P0CX86
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 44
25S ribosomal RNA	RA [auth 1]	3,396	Saccharomyces cerevisiae BY4741
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Molecule	Chains	Length	Organism
Entity ID: 45
5.8S rRNA	SA [auth 3]	158	Saccharomyces cerevisiae BY4741
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Molecule	Chains	Length	Organism
Entity ID: 49
5S rRNA	WA [auth 2]	121	Saccharomyces cerevisiae BY4741
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain EB [auth m] MOL2 format, chain EB [auth m] mmCIF format, chain EB [auth m]	EB [auth m]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain EB [auth m] Interactions & Density Focus chain EB [auth m]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain GB [auth m] MOL2 format, chain GB [auth m] mmCIF format, chain GB [auth m]	GB [auth m]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain GB [auth m] Interactions & Density Focus chain GB [auth m]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain FB [auth m] MOL2 format, chain FB [auth m] mmCIF format, chain FB [auth m]	FB [auth m]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain FB [auth m] Interactions & Density Focus chain FB [auth m]

Non-standard Monomers 1 Unique
ID	Chains	Type	Formula	2D Diagram
UNK Query on UNK	QA [auth K]	L-PEPTIDE LINKING	C₄ H₉ N O₂

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.85 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Zhao, Y.

Li, H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM124622
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM152081

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release

9YWB | pdb_00009ywb

Hypomethylated nucleoplasmic pre-60S intermediate containing Nog2 at Rsa4-arrested 5S post-rotation state

Literature

2'-O-methylation regulates ribosome biogenesis

Biological Assembly 1

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