4D81

Metallosphera sedula Vps4 crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.263 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

Asymmetric Ring Structure of Vps4 Required for Escrt-III Disassembly.

Caillat, C.Macheboeuf, P.Wu, Y.Mccarthy, A.A.Boeri-Erba, E.Effantin, G.Gottlinger, H.G.Weissenhorn, W.Renesto, P.

(2015) Nat Commun 6: 8781

  • DOI: https://doi.org/10.1038/ncomms9781
  • Primary Citation of Related Structures:  
    4D80, 4D81, 4D82

  • PubMed Abstract: 

    The vacuolar protein sorting 4 AAA-ATPase (Vps4) recycles endosomal sorting complexes required for transport (ESCRT-III) polymers from cellular membranes. Here we present a 3.6-Å X-ray structure of ring-shaped Vps4 from Metallosphera sedula (MsVps4), seen as an asymmetric pseudohexamer. Conserved key interface residues are shown to be important for MsVps4 assembly, ATPase activity in vitro, ESCRT-III disassembly in vitro and HIV-1 budding. ADP binding leads to conformational changes within the protomer, which might propagate within the ring structure. All ATP-binding sites are accessible and the pseudohexamer binds six ATP with micromolar affinity in vitro. In contrast, ADP occupies one high-affinity and five low-affinity binding sites in vitro, consistent with conformational asymmetry induced on ATP hydrolysis. The structure represents a snapshot of an assembled Vps4 conformation and provides insight into the molecular motions the ring structure undergoes in a concerted action to couple ATP hydrolysis to ESCRT-III substrate disassembly.


  • Organizational Affiliation

    Unit of Virus-Host Cell interactions (UVHCI), University of Grenoble Alpes, F-38042 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AAA ATPase, central domain protein283Metallosphaera sedulaMutation(s): 0 
Gene Names: HA72_1672MsedA_1706MsedB_1708MsedC_1706MsedD_1707MsedE_1709
UniProt
Find proteins for A4YHC5 (Metallosphaera sedula (strain ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2))
Explore A4YHC5 
Go to UniProtKB:  A4YHC5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4YHC5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.263 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.269α = 90
b = 65.269β = 90
c = 112.521γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 2.0: 2024-05-08
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary