7R72

State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 local model


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.

Cruz, V.E.Sekulski, K.Peddada, N.Sailer, C.Balasubramanian, S.Weirich, C.S.Stengel, F.Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

  • DOI: https://doi.org/10.1038/s41594-022-00874-9
  • Primary Citation of Related Structures:  
    7NAC, 7NAD, 7NAF, 7R6K, 7R6Q, 7R72, 7R7A, 7R7C, 7U0H

  • PubMed Abstract: 

    DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-specific remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize Spb4 in a post-catalytic, high-energy intermediate that drives the organization of the three-way junction at the base of rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly.


  • Organizational Affiliation

    Department of Biophysics, UT Southwestern Medical Center - ND10.124B, Dallas, TX, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 2C [auth 8]710Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3D [auth B]387Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AE [auth G]256Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex-associated protein 3F [auth I]663Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AG [auth P]184Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AH [auth R]189Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AI [auth U]121Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25J [auth X]142Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AK [auth Z]136Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1L [auth b]647Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30M [auth c]105Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AN [auth d]113Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AO [auth g]121Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AP [auth j]88Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38Q [auth k]78Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ERB1R [auth m]429Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pescadillo homologS [auth n]104Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein YTM1T [auth p]460Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP7U [auth t]322Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24V [auth u]199Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferaseW [auth w]841Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 2.1.1.167
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent rRNA helicase SPB4X [auth x]606Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 3.6.4.13
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
25S rRNAA [auth 1]641Saccharomyces cerevisiae BY4741
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Entity ID: 2
MoleculeChains LengthOrganismImage
5.8S rRNAB [auth 2]72Saccharomyces cerevisiae BY4741
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
Y [auth g]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM135617-01
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR150074
Robert A. Welch FoundationUnited StatesI-1897

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references
  • Version 1.2: 2022-12-21
    Changes: Database references
  • Version 1.3: 2022-12-28
    Changes: Database references
  • Version 1.4: 2024-06-05
    Changes: Data collection