2ZME

Integrated structural and functional model of the human ESCRT-II complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Integrated structural model and membrane targeting mechanism of the human ESCRT-II complex

Im, Y.J.Hurley, J.H.

(2008) Dev Cell 14: 902-913

  • DOI: https://doi.org/10.1016/j.devcel.2008.04.004
  • Primary Citation of Related Structures:  
    2ZME, 3CUQ

  • PubMed Abstract: 

    ESCRT-II plays a pivotal role in receptor downregulation and multivesicular body biogenesis and is conserved from yeast to humans. The crystal structures of two human ESCRT-II complex structures have been determined at 2.6 and 2.9 A resolution, respectively. The complex has three lobes and contains one copy each of VPS22 and VPS36 and two copies of VPS25. The structure reveals a dynamic helical domain to which both the VPS22 and VPS36 subunits contribute that connects the GLUE domain to the rest of the ESCRT-II core. Hydrodynamic analysis shows that intact ESCRT-II has a compact, closed conformation. ESCRT-II binds to the ESCRT-I VPS28 C-terminal domain subunit through a helix immediately C-terminal to the VPS36-GLUE domain. ESCRT-II is targeted to endosomal membranes by the lipid-binding activities of both the Vps36 GLUE domain and the first helix of Vps22. These data provide a unifying structural and functional framework for the ESCRT-II complex.


  • Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar-sorting protein SNF8258Homo sapiensMutation(s): 0 
Gene Names: SNF8EAP30
UniProt & NIH Common Fund Data Resources
Find proteins for Q96H20 (Homo sapiens)
Explore Q96H20 
Go to UniProtKB:  Q96H20
PHAROS:  Q96H20
GTEx:  ENSG00000159210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96H20
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein-sorting-associated protein 36238Homo sapiensMutation(s): 0 
Gene Names: VPS36C13orf9EAP45
UniProt & NIH Common Fund Data Resources
Find proteins for Q86VN1 (Homo sapiens)
Explore Q86VN1 
Go to UniProtKB:  Q86VN1
PHAROS:  Q86VN1
GTEx:  ENSG00000136100 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86VN1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein-sorting-associated protein 25
C, D
102Homo sapiensMutation(s): 0 
Gene Names: VPS25DERP9EAP20
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRG1 (Homo sapiens)
Explore Q9BRG1 
Go to UniProtKB:  Q9BRG1
PHAROS:  Q9BRG1
GTEx:  ENSG00000131475 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BRG1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.219 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.48α = 90
b = 81.48β = 90
c = 226.244γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description