7D5T

Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1)

PDB DOI: https://doi.org/10.2210/pdb7D5T/pdb
NAKB: 7D5T
EM Map EMD-30585: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Saccharomyces cerevisiae S288C
Mutation(s): No

Deposited: 2020-09-28 Released: 2021-10-06
Deposition Author(s): Du, Y., Zhang, J., An, W., Ye, K.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.00 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

Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1)

Ye, K.

To be published.

Macromolecule Content

Total Structure Weight: 4,020.5 kDa
Atom Count: 163,485
Modelled Residue Count: 18,869
Deposited Residue Count: 30,273
Unique protein chains: 50
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S1-A	D [auth SC]	255	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33442 Go to UniProtKB: P33442
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UniProt Group	P33442
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S4-A	E [auth SF]	261	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX35 Go to UniProtKB: P0CX35
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UniProt Group	P0CX35
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S5	F [auth SG]	225	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26783 Go to UniProtKB: P26783
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UniProt Group	P26783
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S6-A	G [auth SH]	236	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX37 Go to UniProtKB: P0CX37
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UniProt Group	P0CX37
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S7-A	H [auth SI]	190	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26786 Go to UniProtKB: P26786
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UniProt Group	P26786
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S8-A	I [auth SJ]	200	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX39 Go to UniProtKB: P0CX39
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CX39
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S9-A	J [auth SK]	197	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore O13516 Go to UniProtKB: O13516
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UniProt Group	O13516
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S11-A	K [auth SM]	156	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX47 Go to UniProtKB: P0CX47
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UniProt Group	P0CX47
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S13	L [auth SO]	151	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05756 Go to UniProtKB: P05756
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UniProt Group	P05756
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S14-A	M [auth SP]	137	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06367 Go to UniProtKB: P06367
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UniProt Group	P06367
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S16-A	N [auth SR]	143	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX51 Go to UniProtKB: P0CX51
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UniProt Group	P0CX51
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S22-B	O [auth SX]	130	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q3E7Y3 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E7Y3 Go to UniProtKB: Q3E7Y3
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UniProt Group	Q3E7Y3
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S23-A	P [auth SY]	145	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX29 Go to UniProtKB: P0CX29
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UniProt Group	P0CX29
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S24-A	Q [auth SZ]	135	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX31 Go to UniProtKB: P0CX31
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UniProt Group	P0CX31
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S27-A	R [auth Sc]	82	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35997 Go to UniProtKB: P35997
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UniProt Group	P35997
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S28-A	S [auth Sd]	67	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E7X9 Go to UniProtKB: Q3E7X9
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UniProt Group	Q3E7X9
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA 2'-O-methyltransferase fibrillarin	T [auth 3B], U [auth 3C]	327	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.1.1
UniProt
Find proteins for P15646 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P15646 Go to UniProtKB: P15646
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15646
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleolar protein 56	V [auth 3D]	504	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12460 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12460 Go to UniProtKB: Q12460
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UniProt Group	Q12460
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleolar protein 58	W [auth 3E]	511	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12499 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12499 Go to UniProtKB: Q12499
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12499
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA-processing protein 9	X [auth 3F]	573	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q06506 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06506 Go to UniProtKB: Q06506
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UniProt Group	Q06506
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
13 kDa ribonucleoprotein-associated protein	Y [auth 3G], Z [auth 3H]	126	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39990 Go to UniProtKB: P39990
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UniProt Group	P39990
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 5	AA [auth A5]	643	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q04177 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04177 Go to UniProtKB: Q04177
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UniProt Group	Q04177
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 10	BA [auth AE]	1,769	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P42945 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P42945 Go to UniProtKB: P42945
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UniProt Group	P42945
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
NET1-associated nuclear protein 1	CA [auth AG]	896	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q02931 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02931 Go to UniProtKB: Q02931
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UniProt Group	Q02931
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Periodic tryptophan protein 2	DA [auth B1]	900	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P25635 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25635 Go to UniProtKB: P25635
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25635
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 12	EA [auth B2]	943	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12220 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12220 Go to UniProtKB: Q12220
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12220
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 13	FA [auth B3]	817	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q05946 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05946 Go to UniProtKB: Q05946
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UniProt Group	Q05946
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 18	GA [auth B8]	594	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P40362 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40362 Go to UniProtKB: P40362
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UniProt Group	P40362
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 21	HA [auth BE]	939	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q06078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06078 Go to UniProtKB: Q06078
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UniProt Group	Q06078
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 6	IA [auth B6]	440	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q02354 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02354 Go to UniProtKB: Q02354
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UniProt Group	Q02354
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 7	JA [auth 5C]	554	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P40055 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40055 Go to UniProtKB: P40055
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UniProt Group	P40055
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 11	KA [auth 5D]	250	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P34247 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34247 Go to UniProtKB: P34247
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UniProt Group	P34247
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein MPP10	LA [auth 5E]	593	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P47083 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47083 Go to UniProtKB: P47083
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UniProt Group	P47083
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar ribonucleoprotein protein IMP3	MA [auth 5F]	183	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P32899 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32899 Go to UniProtKB: P32899
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UniProt Group	P32899
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar ribonucleoprotein protein IMP4	NA [auth 5G]	290	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P53941 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53941 Go to UniProtKB: P53941
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UniProt Group	P53941
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Something about silencing protein 10	OA [auth 5H]	610	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12136 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12136 Go to UniProtKB: Q12136
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UniProt Group	Q12136
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SOF1	PA [auth 5I]	489	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P33750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33750 Go to UniProtKB: P33750
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UniProt Group	P33750
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA-processing protein FCF2	QA [auth 5J]	217	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12035 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12035 Go to UniProtKB: Q12035
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UniProt Group	Q12035
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA-processing protein FCF1	RA [auth 5K]	189	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q05498 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05498 Go to UniProtKB: Q05498
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UniProt Group	Q05498
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA biogenesis protein RRP5	SA [auth RD]	1,729	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q05022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05022 Go to UniProtKB: Q05022
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UniProt Group	Q05022
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 22	TA [auth RE]	1,237	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P53254 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53254 Go to UniProtKB: P53254
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UniProt Group	P53254
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA-processing protein 7	UA [auth RF]	297	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P25368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25368 Go to UniProtKB: P25368
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UniProt Group	P25368
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome biogenesis protein BMS1	VA [auth RJ]	1,183	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q08965 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08965 Go to UniProtKB: Q08965
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UniProt Group	Q08965
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA 3'-terminal phosphate cyclase-like protein	WA [auth RK]	367	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08096 Go to UniProtKB: Q08096
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UniProt Group	Q08096
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleolar complex protein 14	XA [auth RN]	810	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q99207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q99207 Go to UniProtKB: Q99207
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UniProt Group	Q99207
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 20	YA [auth RP]	2,493	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P35194 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35194 Go to UniProtKB: P35194
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UniProt Group	P35194
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 14	ZA [auth RQ]	899	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q04500 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04500 Go to UniProtKB: Q04500
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UniProt Group	Q04500
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Reference Sequence

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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
Pno1	AB [auth RT]	326	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent RNA helicase DHR1	BB [auth RZ]	1,267	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.6.4.13
UniProt
Find proteins for Q04217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04217 Go to UniProtKB: Q04217
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UniProt Group	Q04217
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned peptides 1	CB [auth X1]	300	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Entity ID: 1
Molecule	Chains	Length	Organism	Image
U3 snoRNA	A [auth 3A]	333	Saccharomyces cerevisiae S288C
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Entity ID: 2
Molecule	Chains	Length	Organism	Image
5' ETS	B [auth 5A]	700	Saccharomyces cerevisiae S288C
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Entity ID: 3
Molecule	Chains	Length	Organism	Image
18S rRNA	C [auth SA]	1,812	Saccharomyces cerevisiae S288C
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Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain FB [auth RJ] MOL2 format, chain FB [auth RJ]	FB [auth RJ]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain FB [auth RJ] Interactions & Density Focus chain FB [auth RJ]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain HB [auth RZ] MOL2 format, chain HB [auth RZ]	HB [auth RZ]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain HB [auth RZ] Interactions & Density Focus chain HB [auth RZ]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain DB [auth Sc] SDF format, chain EB [auth 5K] MOL2 format, chain DB [auth Sc] MOL2 format, chain EB [auth 5K]	DB [auth Sc], EB [auth 5K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DB [auth Sc] Focus chain EB [auth 5K] Interactions & Density Focus chain DB [auth Sc] Focus chain EB [auth 5K]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain GB [auth RJ] MOL2 format, chain GB [auth RJ]	GB [auth RJ]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain GB [auth RJ] Interactions & Density Focus chain GB [auth RJ]