4Y2D

Crystal structure of the mCD1d/7DW8-5/iNKTCR ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.1 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1
A, E
285Mus musculusMutation(s): 1 
Gene Names: Cd1d1Cd1.1
UniProt & NIH Common Fund Data Resources
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Go to UniProtKB:  P11609
IMPC:  MGI:107674
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UniProt GroupP11609
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, F
99Mus musculusMutation(s): 0 
Gene Names: B2m
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IMPC:  MGI:88127
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UniProt GroupP01887
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
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: Trav11Trav11d
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Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
Find proteins for A0A0B4J1J9 (Mus musculus)
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Go to UniProtKB:  A0A0B4J1J9
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UniProt GroupsP01848A0A0B4J1J9
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
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: TRBC2TCRBC2
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Go to UniProtKB:  A0A5B9
PHAROS:  A0A5B9
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UniProt GroupsA0A5B9A2NTY6
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Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7DW
Query on 7DW

Download Ideal Coordinates CCD File 
M [auth A],
Q [auth E]
11-(4-fluorophenyl)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide
C41 H72 F N O9
GIXLTJURKGIRDL-IWVUWWQKSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
O [auth E],
P [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUC
Query on FUC

Download Ideal Coordinates CCD File 
N [auth E]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.422α = 90
b = 150.264β = 96.24
c = 100.8γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI074952

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 2.0: 2017-11-29
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2019-12-11
    Changes: Author supporting evidence, Data collection
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary