3O8X
Recognition of Glycolipid Antigen by iNKT Cell TCR
- PDB DOI: https://doi.org/10.2210/pdb3O8X/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus, Homo sapiens
- Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
- Mutation(s): Yes 
- Deposited: 2010-08-03 Released: 2010-09-29 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.74 Å
- R-Value Free: 0.253 
- R-Value Work: 0.195 
- R-Value Observed: 0.198 
This is version 2.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Antigen-presenting glycoprotein CD1d1 | 285 | Mus musculus | Mutation(s): 1  Gene Names: Cd1d1, Cd1.1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P11609 (Mus musculus) Explore P11609  Go to UniProtKB:  P11609 | |||||
IMPC:  MGI:107674 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P11609 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Beta-2-microglobulin | 99 | Mus musculus | Mutation(s): 0  Gene Names: B2m | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887 | |||||
IMPC:  MGI:88127 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01887 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Valpha14 chimera (Mouse variable domain, Human T-cell receptor alpha chain C region constant domain) | 209 | Mus musculus, Homo sapiens This entity is chimeric | Mutation(s): 1  Gene Names: TRAC, TCRA | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848 | |||||
PHAROS:  P01848 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01848 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Vbeta8.2 chimera (Mouse variable domain, Human T-cell receptor beta-2 chain C region constant domain) | 241 | Mus musculus, Homo sapiens This entity is chimeric | Mutation(s): 2  Gene Names: TRBC2, TCRBC2 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for A0A5B9 (Homo sapiens) Explore A0A5B9  Go to UniProtKB:  A0A5B9 | |||||
PHAROS:  A0A5B9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A5B9 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GSL Query on GSL | G [auth A] | (2S,3R)-3-HYDROXY-2-(TETRADECANOYLAMINO)OCTADECYL ALPHA-D-GALACTOPYRANOSIDURONIC ACID C38 H73 N O9 IRPOZWRRAFKYMQ-LMIAXWKISA-N | |||
NAG Query on NAG | H [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.74 Å
- R-Value Free: 0.253 
- R-Value Work: 0.195 
- R-Value Observed: 0.198 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 79 | α = 90 |
b = 191.2 | β = 90 |
c = 151.2 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2010-09-29  Deposition Author(s): Zajonc, D.M., Li, Y.
Revision History (Full details and data files)
- Version 1.0: 2010-09-29
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-06-21
Changes: Database references, Source and taxonomy, Structure summary - Version 1.3: 2017-06-28
Changes: Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-07-26
Changes: Database references, Structure summary - Version 2.2: 2023-09-06
Changes: Data collection, Refinement description