4BX9

Human Vps33A in complex with a fragment of human Vps16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of Vps33A recruitment to the human HOPS complex by Vps16.

Graham, S.C.Wartosch, L.Gray, S.R.Scourfield, E.J.Deane, J.E.Luzio, J.P.Owen, D.J.

(2013) Proc Natl Acad Sci U S A 110: 13345-13350

  • DOI: 10.1073/pnas.1307074110
  • Primary Citation of Related Structures:  
    4BX8, 4BX9

  • PubMed Abstract: 
  • The multisubunit homotypic fusion and vacuole protein sorting (HOPS) membrane-tethering complex is required for late endosome-lysosome and autophagosome-lysosome fusion in mammals. We have determined the crystal structure of the human HOPS subunit Vps33A, confirming its identity as a Sec1/Munc18 family member ...

    The multisubunit homotypic fusion and vacuole protein sorting (HOPS) membrane-tethering complex is required for late endosome-lysosome and autophagosome-lysosome fusion in mammals. We have determined the crystal structure of the human HOPS subunit Vps33A, confirming its identity as a Sec1/Munc18 family member. We show that HOPS subunit Vps16 recruits Vps33A to the human HOPS complex and that residues 642-736 are necessary and sufficient for this interaction, and we present the crystal structure of Vps33A in complex with Vps16(642-736). Mutations at the binding interface disrupt the Vps33A-Vps16 interaction both in vitro and in cells, preventing recruitment of Vps33A to the HOPS complex. The Vps33A-Vps16 complex provides a structural framework for studying the association between Sec1/Munc18 proteins and tethering complexes.


    Organizational Affiliation

    Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom. scg34@cam.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33AA, B606Homo sapiensMutation(s): 0 
Gene Names: VPS33A
UniProt & NIH Common Fund Data Resources
Find proteins for Q96AX1 (Homo sapiens)
Explore Q96AX1 
Go to UniProtKB:  Q96AX1
PHAROS:  Q96AX1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 16 HOMOLOGC99Homo sapiensMutation(s): 0 
Gene Names: VPS16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H269 (Homo sapiens)
Explore Q9H269 
Go to UniProtKB:  Q9H269
PHAROS:  Q9H269
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMR
Query on LMR

Download Ideal Coordinates CCD File 
E [auth A](2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
 Ligand Interaction
MLA
Query on MLA

Download Ideal Coordinates CCD File 
H [auth C]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
D [auth A], F [auth B], G [auth B]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.41α = 90
b = 128.41β = 90
c = 263.36γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-08-14
    Changes: Database references
  • Version 1.2: 2013-09-25
    Changes: Database references
  • Version 1.3: 2015-04-22
    Changes: Non-polymer description
  • Version 1.4: 2019-03-13
    Changes: Data collection, Database references, Experimental preparation, Other