2CAY

Vps36 N-terminal PH domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Escrt-I Core and Escrt-II Glue Domain Structures Reveal Role for Glue in Linking to Escrt-I and Membranes.

Teo, H.Gill, D.J.Sun, J.Perisic, O.Veprintsev, D.B.Wallis, Y.Emr, S.D.Williams, R.L.

(2006) Cell 125: 99

  • DOI: 10.1016/j.cell.2006.01.047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ESCRT complexes form the main machinery driving protein sorting from endosomes to lysosomes. Currently, the picture regarding assembly of ESCRTs on endosomes is incomplete. The structure of the conserved heterotrimeric ESCRT-I core presented here sho ...

    ESCRT complexes form the main machinery driving protein sorting from endosomes to lysosomes. Currently, the picture regarding assembly of ESCRTs on endosomes is incomplete. The structure of the conserved heterotrimeric ESCRT-I core presented here shows a fan-like arrangement of three helical hairpins, each corresponding to a different subunit. Vps23/Tsg101 is the central hairpin sandwiched between the other subunits, explaining the critical role of its "steadiness box" in the stability of ESCRT-I. We show that yeast ESCRT-I links directly to ESCRT-II, through a tight interaction of Vps28 (ESCRT-I) with the yeast-specific zinc-finger insertion within the GLUE domain of Vps36 (ESCRT-II). The crystal structure of the GLUE domain missing this insertion reveals it is a split PH domain, with a noncanonical lipid binding pocket that binds PtdIns3P. The simultaneous and reinforcing interactions of ESCRT-II GLUE domain with membranes, ESCRT-I, and ubiquitin are critical for ubiquitinated cargo progression from early to late endosomes.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Medical Research Council Centre, Cambridge, CB2 2QH, United Kingdom. hlt@mrc-lmb.cam.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VACUOLAR PROTEIN SORTING PROTEIN 36
A, B
145Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VPS36 (GRD12, VAC3, VPL11)
Find proteins for Q06696 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: VPS36
Go to UniProtKB:  Q06696
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.451α = 90.00
b = 88.375β = 90.00
c = 45.888γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
SnBphasing
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-05
    Type: Refinement description
  • Version 1.4: 2018-01-24
    Type: Source and taxonomy