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: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein 15
E
220Saccharomyces 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 L3
F
387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
I
176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
K
256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Nucleolar protein 7
M
605Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP7RRP13YPH1YGR103W
Find proteins for P53261 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosome production factor 1
O
295Saccharomyces 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-A
P
199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
Q
138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
S
199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
U
186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
W
172Saccharomyces 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 1
X
278Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP1YDR087CD4478
Find proteins for P35178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase HAS1
Y
505Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HAS1YMR290C
EC: 3.6.4.13
Find proteins for Q03532 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Protein MAK16
Z
306Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MAK16YAL025C
Find proteins for P10962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein BRX1
a
291Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRX1YOL077C
Find proteins for Q08235 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
rRNA-processing protein EBP2
b
427Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EBP2YKL172WYKL636
Find proteins for P36049 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
c
127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Unassigned
d
154Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
i
130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
m
100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
J
244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
L
191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 6
N
245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF6CDC95YPR016CLPZ15C
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
R
204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
T
184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein NSA1
V
463Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSA1YGL111WG2990
Find proteins for P53136 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
j
107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
l
120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
n
88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein RLP7
D
322Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP7RPL7YNL002CN2014
Find proteins for P40693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
G
362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome-interacting protein CIC1
H
376Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CIC1NSA3YHR052W
Find proteins for P38779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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

View Full Validation Report



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