5NHT

human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2

• PDB DOI: https://doi.org/10.2210/pdb5NHT/pdb

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


• Deposited: 2017-03-22 Released: 2018-05-16 
• Deposition Author(s): Exertier, C., Reiser, J.-B., Lantez, V., Chouquet, A., Bonneville, M., Saulquin, X., Housset, D.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.299 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 

Literature

human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2

Exertier, C., Reiser, J.-B., Housset, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 96.44 kDa 
• Atom Count: 6,613 
• Modelled Residue Count: 825 
• Deposited Residue Count: 848 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	A [auth H]	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B [auth L]	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Melanoma antigen recognized by T-cells 1	C [auth P]	10	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q16655 (Homo sapiens) Explore Q16655  Go to UniProtKB:  Q16655
PHAROS:  Q16655 GTEx:  ENSG00000120215

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell receptor alpha variable 12-2,T-cell receptor, sp3.4 alpha chain	D [auth A]	211	Homo sapiens	Mutation(s): 0  Gene Names: TRAV12-2
UniProt & NIH Common Fund Data Resources
Find proteins for K7N5N2 (Homo sapiens) Explore K7N5N2  Go to UniProtKB:  K7N5N2
Find proteins for A0A075B6T6 (Homo sapiens) Explore A0A075B6T6  Go to UniProtKB:  A0A075B6T6
PHAROS:  A0A075B6T6 GTEx:  ENSG00000211789
UniProt Groups	K7N5N2A0A075B6T6

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell receptor beta variable 19,TRB protein	E [auth B]	251	Homo sapiens	Mutation(s): 0  Gene Names: TCRBV17S1A1T, TRBV19, TRB
UniProt
Find proteins for A0A5B3 (Homo sapiens) Explore A0A5B3  Go to UniProtKB:  A0A5B3
Find proteins for A0A0C4ZKA8 (Homo sapiens) Explore A0A0C4ZKA8  Go to UniProtKB:  A0A0C4ZKA8
UniProt Groups	A0A0C4ZKA8A0A5B3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SCN	F [auth H]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
K	G [auth H], H	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	I [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.299 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 222.077	α = 90
b = 49.284	β = 97.61
c = 96.133	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-16 
Deposition Author(s): Exertier, C., Reiser, J.-B., Lantez, V., Chouquet, A., Bonneville, M., Saulquin, X., Housset, D.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-11-BSV3-0006

Revision History  

• Version 1.0: 2018-05-16
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description