2F6M

Structure of a Vps23-C:Vps28-N subcomplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural and functional organization of the ESCRT-I trafficking complex.

Kostelansky, M.S.Sun, J.Lee, S.Kim, J.Ghirlando, R.Hierro, A.Emr, S.D.Hurley, J.H.

(2006) Cell 125: 113-126

  • DOI: 10.1016/j.cell.2006.01.049
  • Primary Citation of Related Structures:  
    2F66, 2F6M

  • PubMed Abstract: 
  • The endosomal sorting complex required for transport (ESCRT) complexes are central to receptor downregulation, lysosome biogenesis, and budding of HIV. The yeast ESCRT-I complex contains the Vps23, Vps28, and Vps37 proteins, and its assembly is directed by the C-terminal steadiness box of Vps23, the N-terminal half of Vps28, and the C-terminal half of Vps37 ...

    The endosomal sorting complex required for transport (ESCRT) complexes are central to receptor downregulation, lysosome biogenesis, and budding of HIV. The yeast ESCRT-I complex contains the Vps23, Vps28, and Vps37 proteins, and its assembly is directed by the C-terminal steadiness box of Vps23, the N-terminal half of Vps28, and the C-terminal half of Vps37. The crystal structures of a Vps23:Vps28 core subcomplex and the Vps23:Vps28:Vps37 core were solved at 2.1 and 2.8 A resolution. Each subunit contains a structurally similar pair of helices that form the core. The N-terminal domain of Vps28 has a hydrophobic binding site on its surface that is conformationally dynamic. The C-terminal domain of Vps28 binds the ESCRT-II complex. The structure shows how ESCRT-I is assembled by a compact core from which the Vps23 UEV domain, the Vps28 C domain, and other domains project to bind their partners.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permeaseA, C65Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: STP22VPS23
UniProt
Find proteins for P25604 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25604 
Go to UniProtKB:  P25604
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25604
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein VPS28B, D109Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: VPS28VPT28
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
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.239α = 90
b = 119.252β = 90
c = 125.391γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations