5Z3G

Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 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 an early precursor of large ribosomal subunit reveals a half-assembled intermediate.

Zhou, D.Zhu, X.Zheng, S.Tan, D.Dong, M.Q.Ye, K.

(2019) Protein Cell 10: 120-130

  • DOI: 10.1007/s13238-018-0526-7
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Assembly of eukaryotic ribosome is a complicated and dynamic process that involves a series of intermediates. It is unknown how the highly intertwined structure of 60S large ribosomal subunits is established. Here, we report the structure of an early ...

    Assembly of eukaryotic ribosome is a complicated and dynamic process that involves a series of intermediates. It is unknown how the highly intertwined structure of 60S large ribosomal subunits is established. Here, we report the structure of an early nucleolar pre-60S ribosome determined by cryo-electron microscopy at 3.7 Å resolution, revealing a half-assembled subunit. Domains I, II and VI of 25S/5.8S rRNA pack tightly into a native-like substructure, but domains III, IV and V are not assembled. The structure contains 12 assembly factors and 19 ribosomal proteins, many of which are required for early processing of large subunit rRNA. The Brx1-Ebp2 complex would interfere with the assembly of domains IV and V. Rpf1, Mak16, Nsa1 and Rrp1 form a cluster that consolidates the joining of domains I and II. Our structure reveals a key intermediate on the path to establishing the global architecture of 60S subunits.


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing, 100049, China. yekeqiong@ibp.ac.cn.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein RLP7D322Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP7RPL7YNL002CN2014
Find proteins for P40693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein 15E220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP15YNL110CN1954
Find proteins for P53927 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3F387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-AG362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome-interacting protein CIC1H376Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CIC1NSA3YHR052W
Find proteins for P38779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-AI176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-AJ244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-AK256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-AL191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Nucleolar protein 7M605Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP7RRP13YPH1YGR103W
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 6N245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF6CDC95YPR016CLPZ15C
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosome production factor 1O295Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPF1YHR088W
Find proteins for P38805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-AP199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-AQ138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-AR204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-AS199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-AT184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-AU186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein NSA1V463Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSA1YGL111WG2990
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-AW172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA-processing protein 1X278Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP1YDR087CD4478
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase HAS1Y505Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HAS1YMR290C
EC: 3.6.4.13
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Protein MAK16Z306Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MAK16YAL025C
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein BRX1a291Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRX1YOL077C
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
rRNA-processing protein EBP2b427Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EBP2YKL172WYKL636
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-Ac127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Unassignedd154Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32i130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-Aj107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-Al120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-Am100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-An88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 1
MoleculeChainsLengthOrganism
25S rRNAA3396Saccharomyces cerevisiae

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Entity ID: 2
MoleculeChainsLengthOrganism
5.8S rRNAB158Saccharomyces cerevisiae

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Entity ID: 3
MoleculeChainsLengthOrganism
ITS2 RNAC232Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2018-01-06 
  • Released Date: 2018-04-11 
  • Deposition Author(s): Zhu, X., Zhou, D., Ye, K.

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other