6C0F

Yeast nucleolar pre-60S ribosomal subunit (state 2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 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

Modular assembly of the nucleolar pre-60S ribosomal subunit.

Sanghai, Z.A.Miller, L.Molloy, K.R.Barandun, J.Hunziker, M.Chaker-Margot, M.Wang, J.Chait, B.T.Klinge, S.

(2018) Nature 556: 126-129

  • DOI: 10.1038/nature26156
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly factors regulate and chaperone the systematic folding o ...

    Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly factors regulate and chaperone the systematic folding of pre-ribosomal RNA subdomains. However, owing to a lack of structural information, the role of these factors during early nucleolar 60S assembly is not fully understood. Here we report cryo-electron microscopy (cryo-EM) reconstructions of the nucleolar pre-60S ribosomal subunit in different conformational states at resolutions of up to 3.4 Å. These reconstructions reveal how steric hindrance and molecular mimicry are used to prevent both premature folding states and binding of later factors. This is accomplished by the concerted activity of 21 ribosome assembly factors that stabilize and remodel pre-ribosomal RNA and ribosomal proteins. Among these factors, three Brix-domain proteins and their binding partners form a ring-like structure at ribosomal RNA (rRNA) domain boundaries to support the architecture of the maturing particle. The existence of mutually exclusive conformations of these pre-60S particles suggests that the formation of the polypeptide exit tunnel is achieved through different folding pathways during subsequent stages of ribosome assembly. These structures rationalize previous genetic and biochemical data and highlight the mechanisms that drive eukaryotic ribosome assembly in a unidirectional manner.


    Organizational Affiliation

    Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein NSA1
A
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: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
B
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: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
C
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: 7
MoleculeChainsSequence LengthOrganismDetails
Protein MAK16
D
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: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
E
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: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
F
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: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
G
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: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosome production factor 1
I
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: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome-interacting protein CIC1
K
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: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
L
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: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
M
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: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
N
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: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
O
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: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
P
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: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
Q
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: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
S
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: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
V
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL23A (RPL17A, RPL17AA)
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL23A
Go to UniProtKB:  P0CX41
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Nucleolar GTP-binding protein 1
W
647Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NOG1
Find proteins for Q02892 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02892
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
Y
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: 23
MoleculeChainsSequence LengthOrganismDetails
Nucleolar protein 16
7
231Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NOP16
Find proteins for P40007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: NOP16
Go to UniProtKB:  P40007
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA-processing protein 14
8
434Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP14
Find proteins for P36080 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36080
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein BRX1
b
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: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
e
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: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
f
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: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
h
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: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
i
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: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
j
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: 31
MoleculeChainsSequence LengthOrganismDetails
Brx1-associated peptide
x
28N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
rRNA-processing protein EBP2
m
74N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Pescadillo homolog
n
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: 34
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein 15
o
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: 35
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase HAS1
p
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: 36
MoleculeChainsSequence LengthOrganismDetails
Protein MAK11
q
285N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein ERB1
s
807Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ERB1
Find proteins for Q04660 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04660
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein RLP7
t
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: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein RLP24
u
199Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RLP24
Find proteins for Q07915 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07915
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein SSF1
v
453Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SSF1
Find proteins for P38789 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38789
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA-processing protein 15
w
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP15
Find proteins for Q06511 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RRP15
Go to UniProtKB:  Q06511
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 6
y
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: 43
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA-processing protein 1
z
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: 1
MoleculeChainsLengthOrganism
Saccharomyces cerevisiae S288c 35S pre-ribosomal RNA miscRNA13395Saccharomyces cerevisiae BY4741
Entity ID: 2
MoleculeChainsLengthOrganism
5.8S rRNA2158Saccharomyces cerevisiae BY4741
Entity ID: 3
MoleculeChainsLengthOrganism
ITS26232Saccharomyces cerevisiae BY4741
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D, j, u
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
b, m, q, s, x
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NIHUnited States1DP2GM123459
Swiss National Science FoundationSwitzerland155515
NIHUnited StatesGM115327-Tan
NIHUnited StatesP41GM103314
NIHUnited StatesP41GM109824

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references