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
Starting Model: experimental
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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 |
---|---|
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 |