4BX9

Human Vps33A in complex with a fragment of human Vps16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.176 

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:  

  • 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 Vp ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33A
A, B
606Homo sapiensMutation(s): 0 
Gene Names: VPS33A
Find proteins for Q96AX1 (Homo sapiens)
Go to Gene View: VPS33A
Go to UniProtKB:  Q96AX1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 16 HOMOLOG
C
99Homo sapiensMutation(s): 0 
Gene Names: VPS16
Find proteins for Q9H269 (Homo sapiens)
Go to Gene View: VPS16
Go to UniProtKB:  Q9H269
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
LMR
Query on LMR

Download SDF File 
Download CCD File 
A
(2S)-2-hydroxybutanedioic acid
L-Malate
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
 Ligand Interaction
MLA
Query on MLA

Download SDF File 
Download CCD File 
C
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.176 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.410α = 90.00
b = 128.410β = 90.00
c = 263.360γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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