2P22

Structure of the Yeast ESCRT-I Heterotetramer Core

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

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This is version 1.7 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
  • Primary Citation of Related Structures:  
    2P22

  • 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 subunits, Vps23, Vps28, Vps37, and Mvb12 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permeaseA174Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VPS23
UniProt
Find proteins for P25604 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P25604
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UniProt GroupP25604
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 28B118Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: VPT28
UniProt
Find proteins for Q02767 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q02767
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UniProt GroupQ02767
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein SRN2C192Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: VPS37
UniProt
Find proteins for Q99176 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q99176
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UniProt GroupQ99176
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic regionD79Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MVB12
UniProt
Find proteins for P42939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P42939 
Go to UniProtKB:  P42939
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UniProt GroupP42939
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.054α = 90
b = 83.766β = 90
c = 269.146γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2015-06-24
    Changes: Data collection
  • Version 1.4: 2017-11-29
    Changes: Database references
  • Version 1.5: 2018-01-24
    Changes: Structure summary
  • Version 1.6: 2020-04-15
    Changes: Data collection, Database references
  • Version 1.7: 2021-10-20
    Changes: Database references, Derived calculations