2P22

Structure of the Yeast ESCRT-I Heterotetramer Core

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 

Literature

Molecular architecture and functional model of the complete yeast ESCRT-I heterotetramer.

Kostelansky, M.S., Schluter, C., Tam, Y.Y., Lee, S., Ghirlando, R., Beach, B., Conibear, E., Hurley, J.H.

(2007) Cell 129: 485-498

  • DOI: 10.1016/j.cell.2007.03.016

  • PubMed Abstract: 

    • The endosomal sorting complex required for transport-I (ESCRT-I) complex, which is conserved from yeast to humans, directs the lysosomal degradation of ubiquitinated transmembrane proteins and the budding of the HIV virus. Yeast ESCRT-I contains four ...

    The endosomal sorting complex required for transport-I (ESCRT-I) complex, which is conserved from yeast to humans, directs the lysosomal degradation of ubiquitinated transmembrane proteins and the budding of the HIV virus. Yeast ESCRT-I contains four subunits, Vps23, Vps28, Vps37, and Mvb12. The crystal structure of the heterotetrameric ESCRT-I complex reveals a highly asymmetric complex of 1:1:1:1 subunit stoichiometry. The core complex is nearly 18 nm long and consists of a headpiece attached to a 13 nm stalk. The stalk is important for cargo sorting by ESCRT-I and is proposed to serve as a spacer regulating the correct disposition of cargo and other ESCRT components. Hydrodynamic constraints and crystallographic structures were used to generate a model of intact ESCRT-I in solution. The results show how ESCRT-I uses a combination of a rigid stalk and flexible tethers to interact with lipids, cargo, and other ESCRT complexes over a span of approximately 25 nm.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
A
174Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: STP22 (VPS23)
Find proteins for P25604 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25604
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 28
B
118Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: VPS28 (VPT28)
Find proteins for Q02767 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: VPS28
Go to UniProtKB:  Q02767
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein SRN2
C
192Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: SRN2 (SRN10, VPS37)
Find proteins for Q99176 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q99176
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
D
79Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MVB12
Find proteins for P42939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P42939
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.233 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 68.054α = 90.00
b = 83.766β = 90.00
c = 269.146γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2015-06-24
    Type: Data collection
  • Version 1.4: 2017-11-29
    Type: Database references
  • Version 1.5: 2018-01-24
    Type: Structure summary