6VME

Human ESCRT-I heterotetramer headpiece


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history


Literature

A helical assembly of human ESCRT-I scaffolds reverse-topology membrane scission.

Flower, T.G.Takahashi, Y.Hudait, A.Rose, K.Tjahjono, N.Pak, A.J.Yokom, A.L.Liang, X.Wang, H.G.Bouamr, F.Voth, G.A.Hurley, J.H.

(2020) Nat Struct Mol Biol 27: 570-580

  • DOI: https://doi.org/10.1038/s41594-020-0426-4
  • Primary Citation of Related Structures:  
    6VME

  • PubMed Abstract: 

    The ESCRT complexes drive membrane scission in HIV-1 release, autophagosome closure, multivesicular body biogenesis, cytokinesis, and other cell processes. ESCRT-I is the most upstream complex and bridges the system to HIV-1 Gag in virus release. The crystal structure of the headpiece of human ESCRT-I comprising TSG101-VPS28-VPS37B-MVB12A was determined, revealing an ESCRT-I helical assembly with a 12-molecule repeat. Electron microscopy confirmed that ESCRT-I subcomplexes form helical filaments in solution. Mutation of VPS28 helical interface residues blocks filament formation in vitro and autophagosome closure and HIV-1 release in human cells. Coarse-grained (CG) simulations of ESCRT assembly at HIV-1 budding sites suggest that formation of a 12-membered ring of ESCRT-I molecules is a geometry-dependent checkpoint during late stages of Gag assembly and HIV-1 budding and templates ESCRT-III assembly for membrane scission. These data show that ESCRT-I is not merely a bridging adaptor; it has an essential scaffolding and mechanical role in its own right.


  • Organizational Affiliation

    Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor susceptibility gene 101 protein81Homo sapiensMutation(s): 0 
Gene Names: TSG101
UniProt & NIH Common Fund Data Resources
Find proteins for Q99816 (Homo sapiens)
Explore Q99816 
Go to UniProtKB:  Q99816
PHAROS:  Q99816
GTEx:  ENSG00000074319 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99816
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 37B71Homo sapiensMutation(s): 0 
Gene Names: VPS37B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9H4 (Homo sapiens)
Explore Q9H9H4 
Go to UniProtKB:  Q9H9H4
PHAROS:  Q9H9H4
GTEx:  ENSG00000139722 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H9H4
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Multivesicular body subunit 12A25Homo sapiensMutation(s): 0 
Gene Names: MVB12ACFBPFAM125A
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EY5 (Homo sapiens)
Explore Q96EY5 
Go to UniProtKB:  Q96EY5
PHAROS:  Q96EY5
GTEx:  ENSG00000141971 
Entity Groups  
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UniProt GroupQ96EY5
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 28 homolog122Homo sapiensMutation(s): 0 
Gene Names: VPS28
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UK41 (Homo sapiens)
Explore Q9UK41 
Go to UniProtKB:  Q9UK41
PHAROS:  Q9UK41
GTEx:  ENSG00000160948 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UK41
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.584α = 90
b = 162.584β = 90
c = 139.715γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR37 AI112442

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-06-03
    Changes: Database references
  • Version 1.2: 2020-06-24
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description