4Y4F
Crystal structure of the mCD1d/GCK127/iNKTCR ternary complex
- PDB DOI: https://doi.org/10.2210/pdb4Y4F/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus, Homo sapiens
- Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
- Mutation(s): Yes 
- Deposited: 2015-02-10 Released: 2015-05-27 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.19 Å
- R-Value Free: 0.257 
- R-Value Work: 0.218 
- R-Value Observed: 0.219 
This is version 2.1 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 |
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain) | 209 | Mus musculus, Homo sapiens This entity is chimeric | Mutation(s): 0  Gene Names: Trav11, Trav11d | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848 | |||||
PHAROS:  P01848 | |||||
Find proteins for A0A0B4J1J9 (Mus musculus) Explore A0A0B4J1J9  Go to UniProtKB:  A0A0B4J1J9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Groups | P01848A0A0B4J1J9 | ||||
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 |
Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain) | 241 | Mus musculus, Homo sapiens This entity is chimeric | Mutation(s): 0  Gene Names: TRBC2, TCRBC2 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for A2NTY6 (Mus musculus) Explore A2NTY6  Go to UniProtKB:  A2NTY6 | |||||
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 Groups | A0A5B9A2NTY6 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
49M Query on 49M | L [auth A], N [auth E] | (1R)-1,5-anhydro-1-[(1E,3S,4S,5R)-4,5-dihydroxy-3-(nonacosanoylamino)nonadec-1-en-1-yl]-D-galactitol C54 H105 N O8 CSICITALHNIXPU-MSSILZRDSA-N | |||
NAG Query on NAG | K [auth A], M [auth E] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.19 Å
- R-Value Free: 0.257 
- R-Value Work: 0.218 
- R-Value Observed: 0.219 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 78.589 | α = 90 |
b = 149.728 | β = 96.46 |
c = 101.386 | γ = 90 |
Software Name | Purpose |
---|---|
Blu-Ice | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |
Coot | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-05-27  Deposition Author(s): Zajonc, D.M., Yu, E.D.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI074952 |
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, Structure summary - Version 1.2: 2019-12-11
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary