7D5T

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

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

Ye, K.

To be published.

Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AD [auth SC]255Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AE [auth SF]261Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5F [auth SG]225Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AG [auth SH]236Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AH [auth SI]190Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AI [auth SJ]200Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AJ [auth SK]197Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AK [auth SM]156Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13L [auth SO]151Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AM [auth SP]137Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AN [auth SR]143Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-BO [auth SX]130Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AP [auth SY]145Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AQ [auth SZ]135Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AR [auth Sc]82Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AS [auth Sd]67Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinT [auth 3B],
U [auth 3C]		327Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1
UniProt
Find proteins for P15646 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 56V [auth 3D]504Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12460 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 58W [auth 3E]511Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12499 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 9X [auth 3F]573Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinY [auth 3G],
Z [auth 3H]		126Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 5AA [auth A5]643Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q04177 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 10BA [auth AE]1,769Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NET1-associated nuclear protein 1CA [auth AG]896Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02931 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Periodic tryptophan protein 2DA [auth B1]900Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 12EA [auth B2]943Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 13FA [auth B3]817Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 18GA [auth B8]594Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 21HA [auth BE]939Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 6IA [auth B6]440Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02354 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 7JA [auth 5C]554Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 11KA [auth 5D]250Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein MPP10LA [auth 5E]593Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P47083 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP3MA [auth 5F]183Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4NA [auth 5G]290Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Something about silencing protein 10OA [auth 5H]610Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12136 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SOF1PA [auth 5I]489Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF2QA [auth 5J]217Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF1RA [auth 5K]189Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q05498 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA biogenesis protein RRP5SA [auth RD]1,729Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q05022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 22TA [auth RE]1,237Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53254 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 7UA [auth RF]297Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P25368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1VA [auth RJ]1,183Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinWA [auth RK]367Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 14XA [auth RN]810Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q99207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 20YA [auth RP]2,493Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P35194 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 14ZA [auth RQ]899Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q04500 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q04500
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UniProt GroupQ04500
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Pno1AB [auth RT]326Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DHR1BB [auth RZ]1,267Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for Q04217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q04217
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UniProt GroupQ04217
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned peptides 1CB [auth X1]300Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
U3 snoRNAA [auth 3A]333Saccharomyces cerevisiae S288C
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Entity ID: 2
MoleculeChains LengthOrganismImage
5' ETSB [auth 5A]700Saccharomyces cerevisiae S288C
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Entity ID: 3
MoleculeChains LengthOrganismImage
18S rRNAC [auth SA]1,812Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
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FB [auth RJ]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ADP
Query on ADP
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HB [auth RZ]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN
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DB [auth Sc],
EB [auth 5K]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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GB [auth RJ]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91940302, 91540201, 31430024, 31325007
Chinese Academy of SciencesChinaXDB08010203

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection, Refinement description