5BW8 | pdb_00005bw8

2.8 A crystal structure of a Get3-Get4-Get5 intermediate complex from S.cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.262 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5BW8

This is version 1.5 of the entry. See complete history

Literature

Mechanism of Assembly of a Substrate Transfer Complex during Tail-anchored Protein Targeting.

Gristick, H.B.Rome, M.E.Chartron, J.W.Rao, M.Hess, S.Shan, S.O.Clemons, W.M.

(2015) J Biological Chem 290: 30006-30017

  • DOI: https://doi.org/10.1074/jbc.M115.677328
  • Primary Citation Related Structures: 
    5BW8, 5BWK

  • PubMed Abstract: 

    Tail-anchored (TA) proteins, defined as having a single transmembrane helix at their C terminus, are post-translationally targeted to the endoplasmic reticulum membrane by the guided entry of TA proteins (GET) pathway. In yeast, the handover of TA substrates is mediated by the heterotetrameric Get4/Get5 complex (Get4/5), which tethers the co-chaperone Sgt2 to the targeting factor, the Get3 ATPase. Binding of Get4/5 to Get3 is critical for efficient TA targeting; however, questions remain about the formation of the Get3·Get4/5 complex. Here we report crystal structures of a Get3·Get4/5 complex from Saccharomyces cerevisiae at 2.8 and 6.0 Å that reveal a novel interface between Get3 and Get4 dominated by electrostatic interactions. Kinetic and mutational analyses strongly suggest that these structures represent an on-pathway intermediate that rapidly assembles and then rearranges to the final Get3·Get4/5 complex. Furthermore, we provide evidence that the Get3·Get4/5 complex is dominated by a single Get4/5 heterotetramer bound to one monomer of a Get3 dimer, uncovering an intriguing asymmetry in the Get4/5 heterotetramer upon Get3 binding. Ultrafast diffusion-limited electrostatically driven Get3·Get4/5 association enables Get4/5 to rapidly sample and capture Get3 at different stages of the GET pathway.


  • Organizational Affiliation
    • From the Division of Chemistry and Chemical Engineering and.

Macromolecule Content 

  • Total Structure Weight: 126.18 kDa 
  • Atom Count: 7,742 
  • Modeled Residue Count: 971 
  • Deposited Residue Count: 1,118 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPase GET3
A, B
373Saccharomyces cerevisiae RM11-1aMutation(s): 0 
Gene Names: GET3SCRG_00595
EC: 3.6
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Golgi to ER traffic protein 4305Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: GET4YOR164CO3580
UniProt
Find proteins for Q12125 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12125 
Go to UniProtKB:  Q12125
Entity Groups
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UniProt GroupQ12125
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-like protein MDY254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MDY2GET5TMA24YOL111C
UniProt
Find proteins for Q12285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12285 
Go to UniProtKB:  Q12285
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12285
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown ProteinE [auth Z]13Saccharomyces cerevisiaeMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.262 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.96α = 90
b = 238.05β = 90
c = 52.19γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Database references
  • Version 1.2: 2015-12-30
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Structure summary