2WOJ | pdb_00002woj

ADP-AlF4 complex of S. cerevisiae GET3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.213 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

The Structural Basis of Tail-Anchored Membrane Protein Recognition by Get3.

Mateja, A.Szlachcic, A.Downing, M.E.Dobosz, M.Mariappan, M.Hegde, R.S.Keenan, R.J.

(2009) Nature 461: 361

  • DOI: https://doi.org/10.1038/nature08319
  • Primary Citation Related Structures: 
    2WOJ, 2WOO

  • PubMed Abstract: 

    Targeting of newly synthesized membrane proteins to the endoplasmic reticulum is an essential cellular process. Most membrane proteins are recognized and targeted co-translationally by the signal recognition particle. However, nearly 5% of membrane proteins are 'tail-anchored' by a single carboxy-terminal transmembrane domain that cannot access the co-translational pathway. Instead, tail-anchored proteins are targeted post-translationally by a conserved ATPase termed Get3. The mechanistic basis for tail-anchored protein recognition or targeting by Get3 is not known. Here we present crystal structures of yeast Get3 in 'open' (nucleotide-free) and 'closed' (ADP.AlF(4)(-)-bound) dimer states. In the closed state, the dimer interface of Get3 contains an enormous hydrophobic groove implicated by mutational analyses in tail-anchored protein binding. In the open state, Get3 undergoes a striking rearrangement that disrupts the groove and shields its hydrophobic surfaces. These data provide a molecular mechanism for nucleotide-regulated binding and release of tail-anchored proteins during their membrane targeting by Get3.


  • Organizational Affiliation
    • Department of Biochemistry & Molecular Biology, The University of Chicago, Gordon Center for Integrative Science, Room W238, 929 East 57th Street, Chicago, Illinois 60637, USA.

Macromolecule Content 

  • Total Structure Weight: 159.92 kDa 
  • Atom Count: 10,014 
  • Modeled Residue Count: 1,190 
  • Deposited Residue Count: 1,416 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPASE GET3
A, B, C, D
354Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.16 (PDB Primary Data), 3.6 (UniProt)
UniProt
Find proteins for Q12154 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12154 
Go to UniProtKB:  Q12154
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12154
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
L [auth C],
P [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ALF

Query on ALF



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B],
M [auth C],
Q [auth D]
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
ZN

Query on ZN



Download:Ideal Coordinates CCD File
H [auth A],
O [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B],
N [auth C],
R [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.213 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.612α = 90
b = 82.628β = 98.28
c = 167.282γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description