4Y4F

Crystal structure of the mCD1d/GCK127/iNKTCR ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural modifications of alphaGalCer in both lipid and carbohydrate moiety influence activation of murine and human iNKT cells

Birkholz, A.Nemcovic, M.Yu, E.D.Girardi, E.Wang, J.Khurana, A.Pauwels, N.Franck, R.W.Tsuji, M.Howell, A.Calenbergh, S.Kronenberg, M.Zajonc, D.M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d1
A, E
285Mus musculusMutation(s): 0 
Gene Names: Cd1d1 (Cd1.1)
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, F
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain)
C, G
209Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Trav11 (Trav11d), TRAC (TCRA)
Find proteins for A0A0B4J1J9 (Mus musculus)
Go to UniProtKB:  A0A0B4J1J9
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
D, H
241Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: TRBC2 (TCRBC2)
Find proteins for A2NTY6 (Mus musculus)
Go to UniProtKB:  A2NTY6
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
49M
Query on 49M

Download SDF File 
Download CCD File 
A, E
(1R)-1,5-anhydro-1-[(1E,3S,4S,5R)-4,5-dihydroxy-3-(nonacosanoylamino)nonadec-1-en-1-yl]-D-galactitol
GCK127
C54 H105 N O8
CSICITALHNIXPU-MSSILZRDSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.589α = 90.00
b = 149.728β = 96.46
c = 101.386γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Blu-Icedata collection
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-10 
  • Released Date: 2015-05-27 
  • Deposition Author(s): Zajonc, D.M., Yu, E.D.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI074952

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary