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 1.1 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
  • Primary Citation of Related Structures:  

  • 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

    Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein RLP7
D
322Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RLP7 (RPL7)
Find proteins for P40693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40693
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein 15
E
220Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NOP15
Find proteins for P53927 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53927
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
F
387Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL3 (MAK8, TCM1)
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL3
Go to UniProtKB:  P14126
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
G
362Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL4A (RPL2, RPL2A)
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P10664
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome-interacting protein CIC1
H
376Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CIC1 (NSA3)
Find proteins for P38779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38779
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
I
176Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL6A (RPL17A, YL16A)
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02326
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
J
244Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL7A (RPL6A, RPL8A, YL8A)
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL7A
Go to UniProtKB:  P05737
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
K
256Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL8A (MAK7, RPL4A)
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17076
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
L
191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL9A (RPL8A, RPL9)
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05738
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Nucleolar protein 7
M
605Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NOP7 (RRP13, YPH1)
Find proteins for P53261 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53261
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 6
N
245Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TIF6 (CDC95)
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12522
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosome production factor 1
O
295Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPF1
Find proteins for P38805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPF1
Go to UniProtKB:  P38805
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
P
199Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL13A
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL13A
Go to UniProtKB:  Q12690
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
Q
138Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL14A
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36105
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
R
204Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL15A (RPL10A, RPL13A, YL10A)
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05748
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
S
199Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL16A (RPL13, RPL21A)
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26784
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
T
184Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL17A (RPL17, RPL20A)
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05740
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
U
186Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL18A (RP28A)
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL18A
Go to UniProtKB:  P0CX49
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein NSA1
V
463Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NSA1
Find proteins for P53136 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53136
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
W
172Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL20A (RPL18A, RPL18A2)
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX23
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA-processing protein 1
X
278Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP1
Find proteins for P35178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RRP1
Go to UniProtKB:  P35178
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase HAS1
Y
505Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HAS1
EC: 3.6.4.13
Find proteins for Q03532 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: HAS1
Go to UniProtKB:  Q03532
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Protein MAK16
Z
306Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MAK16
Find proteins for P10962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MAK16
Go to UniProtKB:  P10962
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein BRX1
a
291Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BRX1
Find proteins for Q08235 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08235
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
rRNA-processing protein EBP2
b
427Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: EBP2
Find proteins for P36049 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36049
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
c
127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL26A (RPL26, RPL33A)
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05743
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Unassigned
d
154N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
i
130Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL32
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL32
Go to UniProtKB:  P38061
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
j
107Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL33A (RPL37A)
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05744
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
l
120Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL35A (SOS1)
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL35A
Go to UniProtKB:  P0CX84
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
m
100Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL36A (RPL39A)
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL36A
Go to UniProtKB:  P05745
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
n
88Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL37A (RPL35A)
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL37A
Go to UniProtKB:  P49166
Entity ID: 1
MoleculeChainsLengthOrganism
25S rRNAA3396Saccharomyces cerevisiae
Entity ID: 2
MoleculeChainsLengthOrganism
5.8S rRNAB158Saccharomyces cerevisiae
Entity ID: 3
MoleculeChainsLengthOrganism
ITS2 RNAC232Saccharomyces cerevisiae
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
d
L-PEPTIDE LINKINGC4 H9 N O2

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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 or Ramachandran Plots



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
    Type: Data collection, Database references