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 6VME | pdb_00006vme

Human ESCRT-I heterotetramer headpiece


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 
    0.240 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6VME

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 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.

Macromolecule Content 

  • Total Structure Weight: 204.22 kDa 
  • Atom Count: 12,786 
  • Modeled Residue Count: 1,576 
  • Deposited Residue Count: 1,794 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  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
Find similar proteins by:|  3D Structure
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H9H4
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Multivesicular body subunit 12A25Homo sapiensMutation(s): 0 
Gene Names: MVB12A, CFBP, FAM125A
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EY5 (Homo sapiens)
Explore Q96EY5 
Go to UniProtKB:  Q96EY5
PHAROS:  Q96EY5
GTEx:  ENSG00000141971 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EY5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free:  0.240 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
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

View Full Validation Report



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