2J9V | pdb_00002j9v

2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.255 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structural Insight Into the Escrt-I/-II Link and its Role in Mvb Trafficking.

Gill, D.J.Teo, H.Sun, J.Perisic, O.Veprintsev, D.B.Emr, S.D.Williams, R.L.

(2007) EMBO J 26: 600

  • DOI: https://doi.org/10.1038/sj.emboj.7601501
  • Primary Citation Related Structures: 
    2J9U, 2J9V, 2J9W

  • PubMed Abstract: 

    ESCRT (endosomal sorting complex required for transport) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs). Yeast ESCRT-I and ESCRT-II interact directly in vitro; however, this association is not detected in yeast cytosol. To gain understanding of the molecular mechanisms of this link, we have characterised the ESCRT-I/-II supercomplex and determined the crystal structure of its interface. The link is formed by the vacuolar protein sorting (Vps)28 C-terminus (ESCRT-I) binding with nanomolar affinity to the Vps36-NZF-N zinc-finger domain (ESCRT-II). A hydrophobic patch on the Vps28-CT four-helix bundle contacts the hydrophobic knuckles of Vps36-NZF-N. Mutation of the ESCRT-I/-II link results in a cargo-sorting defect in yeast. Interestingly, the two Vps36 NZF domains, NZF-N and NZF-C, despite having the same core fold, use distinct surfaces to bind ESCRT-I or ubiquitinated cargo. We also show that a new component of ESCRT-I, Mvb12 (YGR206W), engages ESCRT-I directly with nanomolar affinity to form a 1:1:1:1 heterotetramer. Mvb12 does not affect the affinity of ESCRT-I for ESCRT-II in vitro. Our data suggest a complex regulatory mechanism for the ESCRT-I/-II link in yeast.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Medical Research Council Centre, Cambridge, UK. djg38@mrc-lmb.cam.ac.uk

Macromolecule Content 

  • Total Structure Weight: 11.57 kDa 
  • Atom Count: 870 
  • Modeled Residue Count: 99 
  • Deposited Residue Count: 99 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 2899Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q02767 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02767 
Go to UniProtKB:  Q02767
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02767
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.255 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.69α = 90
b = 128.581β = 90
c = 50.276γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Other, Refinement description