4WVY

Double-heterohexameric rings of full-length Rvb1(ATP)/Rvb2(apo)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.64 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural Basis for Dodecameric Assembly States and Conformational Plasticity of the Full-Length AAA+ ATPases Rvb1Rvb2.

Lakomek, K.Stoehr, G.Tosi, A.Schmailzl, M.Hopfner, K.P.

(2015) Structure 23: 483-495

  • DOI: https://doi.org/10.1016/j.str.2014.12.015
  • Primary Citation of Related Structures:  
    4WVY, 4WW4

  • PubMed Abstract: 

    As building blocks of diverse macromolecular complexes, the AAA+ ATPases Rvb1 and Rvb2 are crucial for many cellular activities including cancer-related processes. Their oligomeric structure and function remain unclear. We report the crystal structures of full-length heteromeric Rvb1·Rvb2 complexes in distinct nucleotide binding states. Chaetomium thermophilum Rvb1·Rvb2 assemble into hexameric rings of alternating molecules and into stable dodecamers. Intriguingly, the characteristic oligonucleotide-binding (OB) fold domains (DIIs) of Rvb1 and Rvb2 occupy unequal places relative to the compact AAA+ core ring. While Rvb1's DII forms contacts between hexamers, Rvb2's DII is rotated 100° outward, occupying lateral positions. ATP was retained bound to Rvb1 but not Rvb2 throughout purification, suggesting nonconcerted ATPase activities and nucleotide binding. Significant conformational differences between nucleotide-free and ATP-/ADP-bound states in the crystal structures and in solution suggest that the functional role of Rvb1·Rvb2 is mediated by highly interconnected structural switches. Our structures provide an atomic framework for dodecameric states and Rvb1·Rvb2's conformational plasticity.


  • Organizational Affiliation

    Department of Biochemistry, Gene Center of the Ludwig-Maximilians University Munich, 81377 Munich, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like 1462Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0006820
UniProt
Find proteins for G0RYI5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0RYI5 
Go to UniProtKB:  G0RYI5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0RYI5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like 2513Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0006170
UniProt
Find proteins for G0RYC2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0RYC2 
Go to UniProtKB:  G0RYC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0RYC2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.64 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.348α = 90
b = 210.348β = 90
c = 137.14γ = 120
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyCollaborative Research Center 1064

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references
  • Version 1.2: 2015-03-11
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description