4WOL

Crystal Structure of the DAP12 transmembrane domain in lipidic cubic phase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/j.celrep.2015.04.045
  • Primary Citation of Related Structures:  

  • 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 prese ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYRO protein tyrosine kinase-binding protein
A, B, C
33Homo sapiensMutation(s): 1 
Gene Names: TYROBP (DAP12, KARAP)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Immune Receptors
Protein: 
DAP12 dimeric signaling domain in complex with activating receptor NKG2C
Find proteins for O43914 (Homo sapiens)
Go to Gene View: TYROBP
Go to UniProtKB:  O43914
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
OLC
Query on OLC

Download SDF File 
Download CCD File 
B, C
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 20.775α = 90.00
b = 35.709β = 90.00
c = 101.070γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)AustraliaGNT1011352
veskiAustraliaVIF12
Australian Research CouncilAustraliaDP110104369, FT120100145

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Data collection, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence