4WO1

Crystal structure of the DAP12 transmembrane domain in lipid cubic phase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.238 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Transmembrane Complexes of DAP12 Crystallized in Lipid Membranes Provide Insights into Control of Oligomerization in Immunoreceptor Assembly.

Knoblich, K.Park, S.Lutfi, M.van 't Hag, L.Conn, C.E.Seabrook, S.A.Newman, J.Czabotar, P.E.Im, W.Call, M.E.Call, M.J.

(2015) Cell Rep 11: 1184-1192

  • DOI: https://doi.org/10.1016/j.celrep.2015.04.045
  • Primary Citation of Related Structures:  
    4WO1, 4WOL

  • PubMed Abstract: 

    The membrane-spanning α helices of single-pass receptors play crucial roles in stabilizing oligomeric structures and transducing biochemical signals across the membrane. Probing intermolecular transmembrane interactions in single-pass receptors presents unique challenges, reflected in a gross underrepresentation of their membrane-embedded domains in structural databases. Here, we present two high-resolution structures of transmembrane assemblies from a eukaryotic single-pass protein crystallized in a lipidic membrane environment. Trimeric and tetrameric structures of the immunoreceptor signaling module DAP12, determined to 1.77-Å and 2.14-Å resolution, respectively, are organized by the same polar surfaces that govern intramembrane assembly with client receptors. We demonstrate that, in addition to the well-studied dimeric form, these trimeric and tetrameric structures are made in cells, and their formation is competitive with receptor association in the ER. The polar transmembrane sequences therefore act as primary determinants of oligomerization specificity through interplay between charge shielding and sequestration of polar surfaces within helix interfaces.


  • Organizational Affiliation

    Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TYRO protein tyrosine kinase-binding protein
A, B, C, D
33Homo sapiensMutation(s): 1 
Gene Names: TYROBPDAP12KARAP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O43914 (Homo sapiens)
Explore O43914 
Go to UniProtKB:  O43914
PHAROS:  O43914
GTEx:  ENSG00000011600 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43914
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.797α = 90
b = 43.685β = 90
c = 50.605γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT1011352
veskiAustraliaVIF12
Australian Research Council (ARC)AustraliaDP110104369, FT120100145

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Advisory, Author supporting evidence, Data collection, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description