3TVM
Structure of the mouse CD1d-SMC124-iNKT TCR complex
- PDB DOI: https://doi.org/10.2210/pdb3TVM/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus, Homo sapiens
- Expression System: Spodoptera frugiperda, Trichoplusia ni, Escherichia coli BL21(DE3)
- Mutation(s): Yes 
- Deposited: 2011-09-20 Released: 2012-02-01 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.273 
- R-Value Work: 0.224 
- R-Value Observed: 0.226 
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: Cd1.1, CD1d, Cd1d1 | ||
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): 1  Gene Names: beta-2-microglobulin | ||
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 (mouse variable domain, human constant domain) | 209 | Mus musculus, Homo sapiens This entity is chimeric | Mutation(s): 0  Gene Names: Valpha14 (mouse variable domain, human constant domain) | ||
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 (mouse variable domain, human constant domain) | 241 | Mus musculus, Homo sapiens This entity is chimeric | Mutation(s): 0  Gene Names: Vbeta8.2 (mouse variable domain, human constant domain) | ||
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 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
07P Query on 07P | N [auth A], Q [auth E] | N-[(2S,3R)-10-[(1R,2R)-2-decylcyclopropyl]-1-(alpha-D-galactopyranosyloxy)-3-hydroxydecan-2-yl]hexacosanamide C55 H107 N O8 BCHXWZQXEKOXKQ-IYKQKVLOSA-N | |||
NAG Query on NAG | M [auth A], P [auth E] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
GOL Query on GOL | R [auth E] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
CL Query on CL | O [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.273 
- R-Value Work: 0.224 
- R-Value Observed: 0.226 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 78.97 | α = 90 |
b = 150.57 | β = 96.35 |
c = 101.96 | γ = 90 |
Software Name | Purpose |
---|---|
Blu-Ice | data collection |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
Entry History 
Deposition Data
- Released Date: 2012-02-01  Deposition Author(s): Girardi, E., Li, Y., Zajonc, D.M.
Revision History (Full details and data files)
- Version 1.0: 2012-02-01
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary - Version 2.2: 2024-03-13
Changes: Source and taxonomy, Structure summary