6VM7

SILv44 T cell receptor bound to HLA-A2 presenting gp100 peptide (ITDQVPFSV)

PDB DOI: https://doi.org/10.2210/pdb6VM7/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): No

Deposited: 2020-01-27 Released: 2021-01-20
Deposition Author(s): Smith, A.R., Baker, B.M.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.241
R-Value Work: 0.199
R-Value Observed: 0.202

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner

Smith, A.R., Alonso, J.A., Ayres, C.M., Singh, N.K., Hellman, L.M., Baker, B.M.

(2021) Proc Natl Acad Sci U S A 118: e2018125118

DOI: https://doi.org/10.1073/pnas.2018125118

Macromolecule Content

Total Structure Weight: 95.99 kDa
Atom Count: 6,777
Modelled Residue Count: 822
Deposited Residue Count: 835
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SILv44 T cell receptor alpha chain	A [auth D]	208	Homo sapiens	Mutation(s): 0 Gene Names: TRAV8-1, TRAC
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SILv44 T cell receptor beta chain	B [auth E]	243	Homo sapiens	Mutation(s): 0 Gene Names: TRBV19, TRBC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen, A-2 alpha chain	C [auth A]	275	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A
UniProt
Find proteins for A0A140T913 (Homo sapiens) Explore A0A140T913 Go to UniProtKB: A0A140T913
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A140T913
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	D [auth B]	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 Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Melanocyte protein PMEL	E [auth C]	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P40967 (Homo sapiens) Explore P40967 Go to UniProtKB: P40967
PHAROS: P40967 GTEx: ENSG00000185664
Entity Groups
UniProt Group	P40967
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	F [auth A], G [auth B], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.241
R-Value Work: 0.199
R-Value Observed: 0.202
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.118	α = 90
b = 94.403	β = 90
c = 143.849	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2021-01-20

Deposition Author(s):

Smith, A.R.

Baker, B.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)		--

Revision History (Full details and data files)

Version 1.0: 2021-01-20
Type: Initial release
Version 1.1: 2021-01-27
Changes: Database references
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary