6LQP

Cryo-EM structure of 90S small subunit preribosomes in transition states (State A)

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

  • Deposited: 2020-01-14 Released: 2020-09-16 
  • Deposition Author(s): Du, Y., Ye, K.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states.

Du, Y., An, W., Zhu, X., Sun, Q., Qi, J., Ye, K.

(2020) Science 369: 1477-1481

  • DOI: https://doi.org/10.1126/science.aba9690
  • Primary Citation of Related Structures:  
    6LQP, 6LQQ, 6LQR, 6LQS, 6LQT, 6LQU, 6LQV

  • PubMed Abstract: 

    The 90 S preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 S ribosome. Here, we gained insight into this transition by determining cryo-electron microscopy structures of Saccharomyces cerevisiae intermediates in the path from the 90 S to the pre-40 S The full transition is blocked by deletion of RNA helicase Dhr1. A series of structural snapshots revealed that the excised 5' external transcribed spacer (5' ETS) is degraded within 90 S , driving stepwise disassembly of assembly factors and ribosome maturation. The nuclear exosome, an RNA degradation machine, docks on the 90 S through helicase Mtr4 and is primed to digest the 3' end of the 5' ETS. The structures resolved between 3.2- and 8.6-angstrom resolution reveal key intermediates and the critical role of 5' ETS degradation in 90 S progression.

    • Organizational Affiliation: 

    Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AD [auth SC]255Saccharomyces cerevisiae S288CMutation(s): 0 
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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 
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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 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AI [auth SJ]200Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AJ [auth SK]197Saccharomyces cerevisiae S288CMutation(s): 0 
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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 S12L [auth SN]143Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13M [auth SO]151Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AN [auth SP]137Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AO [auth SR]143Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AP [auth ST]146Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-BQ [auth SX]130Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AR [auth SY]145Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AS [auth SZ]135Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AT [auth Sc]82Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AU [auth Sd]67Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinV [auth 3B],
W [auth 3C]		327Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 56X [auth 3D]504Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 58Y [auth 3E]511Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 9Z [auth 3F]573Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinAA [auth 3G],
BA [auth 3H]		126Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 4CA [auth A4]776Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q06679 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 5DA [auth A5]643Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 8EA [auth A8]713Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 9FA [auth A9]575Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 10GA [auth AE]1,769Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 15HA [auth AF]513Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NET1-associated nuclear protein 1IA [auth AG]896Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Periodic tryptophan protein 2JA [auth B1]923Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 12KA [auth B2]943Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 13LA [auth B3]817Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 18MA [auth B8]594Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 21NA [auth BE]939Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 6OA [auth B6]440Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Bud site selection protein 21PA [auth 5B]214Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for Q08492 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 7QA [auth 5C]554Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 11RA [auth 5D]250Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein MPP10SA [auth 5E]593Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP3TA [auth 5F]183Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4UA [auth 5G]290Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Something about silencing protein 10VA [auth 5H]610Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12136 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SOF1WA [auth 5I]489Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P33750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF2XA [auth 5J]217Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12035 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF1YA [auth 5K]189Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q05498 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ENP2ZA [auth RA]707Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P48234 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein LCP5AB [auth RB]357Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40079 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
KRR1 small subunit processome componentBB [auth RC]316Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P25586 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 22CB [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: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 7DB [auth RF]297Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P25368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1EB [auth RG],
FB [auth RH]		252Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.260
UniProt
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein UTP30GB [auth RI]274Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P36144 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1HB [auth RJ]1,183Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08965 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinIB [auth RK]367Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
RNA cytidine acetyltransferaseJB [auth RL],
KB [auth RM]		1,056Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.3.1
UniProt
Find proteins for P53914 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 14LB [auth RN]810Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q99207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 4MB [auth RO]552Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 20NB [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: 63
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 14OB [auth RQ]899Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Essential nuclear protein 1PB [auth RS]483Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Pno1QB [auth RT]326Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAF1RB [auth RV]346Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of rDNA transcription protein 14SB [auth RW]206Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40470 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BFR2TB [auth RY]534Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q06631 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned helicesUB [auth X1]347Saccharomyces 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 pre-rRNAC [auth SA]1,808Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

  • Released Date: 2020-09-16 
    • Deposition Author(s): Du, Y., Ye, K.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91940302
Chinese Academy of SciencesChinaXDB08010203
National Natural Science Foundation of China (NSFC)China91540201
National Natural Science Foundation of China (NSFC)China31430024
National Natural Science Foundation of China (NSFC)China31325007

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Refinement description