4ELM
Crystal structure of the mouse CD1d-lysosulfatide-Hy19.3 TCR complex
- PDB DOI: https://doi.org/10.2210/pdb4ELM/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2012-04-11 Released: 2012-07-25 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.48 Å
- R-Value Free: 0.265 
- R-Value Work: 0.209 
- R-Value Observed: 0.212 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Antigen-presenting glycoprotein CD1d1 | A, B [auth C] | 285 | Mus musculus | Mutation(s): 0  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 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Beta-2 microglobulin | C [auth B], D | 99 | Mus musculus | Mutation(s): 0  Gene Names: B2m, beta-2-microglobulin, mCG_11606, RP23-34E24.5-001 | |
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 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Hy19.3 TCR alpha chain (mouse variable domain, human constant domain) | 208 | Mus musculus | Mutation(s): 0  Gene Names: Valpha1 (mouse variable domain, human constant domain | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Hy19.3 TCR beta chain (mouse variable domain, human constant domain) | 244 | Mus musculus | Mutation(s): 0  Gene Names: Vbeta16 (mouse variable domain, human constant domain) | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | I | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 6 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | J | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH |
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SGF Query on SGF | M [auth A], Q [auth C] | (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside C24 H47 N O10 S BXSULSOCJNTUJS-YTBMLWRQSA-N | |||
PLM Query on PLM | N [auth A], R [auth C] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N | |||
NAG Query on NAG | K [auth A], L [auth A], O [auth C], P [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.48 Å
- R-Value Free: 0.265 
- R-Value Work: 0.209 
- R-Value Observed: 0.212 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 98.514 | α = 90 |
b = 126.996 | β = 110.53 |
c = 104.349 | γ = 90 |
Software Name | Purpose |
---|---|
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
Entry History 
Deposition Data
- Released Date: 2012-07-25  Deposition Author(s): Girardi, E., Maricic, I., Wang, J., Mac, T.T., Iyer, P., Kumar, V., Zajonc, D.M.
Revision History (Full details and data files)
- Version 1.0: 2012-07-25
Type: Initial release - Version 1.1: 2013-01-09
Changes: Database references - Version 1.2: 2013-02-06
Changes: Non-polymer description - Version 1.3: 2015-08-12
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Structure summary