Structure of the TCR-H2DB ternary complex with melanoma HSF2 neoantigen YGFRNVVHI
Patskovsky, Y., Finnigan, J., Patskovska, L., Newman, J., Bhardwaj, N., Krogsgaard, M.To be published.
Experimental Data Snapshot
wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
H-2 class I histocompatibility antigen, D-B alpha chain | 281 | Mus musculus | Mutation(s): 0  Gene Names: H2-D1 | ||
UniProt | |||||
Find proteins for P01899 (Mus musculus) Explore P01899  Go to UniProtKB:  P01899 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01899 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Beta-2-microglobulin | 100 | Homo sapiens | Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769 | |||||
PHAROS:  P61769 GTEx:  ENSG00000166710  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P61769 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Heat shock factor protein 2 | 9 | Mus musculus | Mutation(s): 1  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P38533 (Mus musculus) Explore P38533  Go to UniProtKB:  P38533 | |||||
IMPC:  MGI:96239 | |||||
Entity Groups   | |||||
UniProt Group | P38533 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
47BE7 TCR alpha chain | 191 | Mus musculus | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 5 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
47BE7 TCR beta chain | 263 | Mus musculus | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Ligands 2 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | L [auth A], Q [auth D], U [auth E], V [auth E] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
GOL Query on GOL | F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 155.439 | α = 90 |
b = 191.71 | β = 90 |
c = 67.811 | γ = 90 |
Software Name | Purpose |
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REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
Aimless | data scaling |
PHASER | phasing |
Funding Organization | Location | Grant Number |
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National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | CA243486 |