8E5T

Yeast co-transcriptional Noc1-Noc2 RNP assembly checkpoint intermediate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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

A co-transcriptional ribosome assembly checkpoint controls nascent large ribosomal subunit maturation.

Sanghai, Z.A.Piwowarczyk, R.Broeck, A.V.Klinge, S.

(2023) Nat Struct Mol Biol 30: 594-599

  • DOI: https://doi.org/10.1038/s41594-023-00947-3
  • Primary Citation of Related Structures:  
    8E5T

  • PubMed Abstract: 

    During transcription of eukaryotic ribosomal DNA in the nucleolus, assembly checkpoints exist that guarantee the formation of stable precursors of small and large ribosomal subunits. While the formation of an early large subunit assembly checkpoint precedes the separation of small and large subunit maturation, its mechanism of action and function remain unknown. Here, we report the cryo-electron microscopy structure of the yeast co-transcriptional large ribosomal subunit assembly intermediate that serves as a checkpoint. The structure provides the mechanistic basis for how quality-control pathways are established through co-transcriptional ribosome assembly factors, that structurally interrogate, remodel and, together with ribosomal proteins, cooperatively stabilize correctly folded pre-ribosomal RNA. Our findings thus provide a molecular explanation for quality control during eukaryotic ribosome assembly in the nucleolus.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein MAK21A [auth 5]1,025Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NOC2 isoform 1B [auth 6]710Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-A362Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MAK16306Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-A176Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-A244Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-A256Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome-interacting protein CIC1H [auth K]376Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AI [auth L]199Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AJ [auth M]138Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AK [auth N]204Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AL [auth Q]186Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AM [auth S]172Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BRX1N [auth b]291Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32O [auth e]130Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AP [auth f]107Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AQ [auth i]100Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein EBP2R [auth m]427Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pescadillo homologS [auth n]605Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein 15T [auth o]220Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase HAS1U [auth p]505Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 3.6.4.13
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ERB1V [auth s]807Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP7W [auth t]322Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 1X [auth z]278Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AY [auth O]199Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 26
MoleculeChains LengthOrganismImage
25S ribosomal RNAZ [auth 1]3,396Saccharomyces cerevisiae BY4741
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Entity ID: 27
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAAA [auth 2]159Saccharomyces cerevisiae BY4741
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Entity ID: 28
MoleculeChains LengthOrganismImage
ITS2 ribosomal RNABA [auth 3]232Saccharomyces cerevisiae BY4741
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
EA [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 1]
BB [auth 1]
CA [auth C]
CB [auth 1]
DA [auth C]
AB [auth 1],
BB [auth 1],
CA [auth C],
CB [auth 1],
DA [auth C],
DB [auth 1],
EB [auth 1],
FA [auth F],
FB [auth 1],
GA [auth 1],
GB [auth 1],
HA [auth 1],
HB [auth 1],
IA [auth 1],
IB [auth 1],
JA [auth 1],
JB [auth 1],
KA [auth 1],
LA [auth 1],
MA [auth 1],
NA [auth 1],
OA [auth 1],
PA [auth 1],
QA [auth 1],
RA [auth 1],
SA [auth 1],
TA [auth 1],
UA [auth 1],
VA [auth 1],
WA [auth 1],
XA [auth 1],
YA [auth 1],
ZA [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.18

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The G. Harold and Leila Y. Mathers FoundationUnited StatesMF-2104-01554
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM143181

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-04-26
    Changes: Database references
  • Version 1.2: 2023-05-31
    Changes: Database references