4EUP | pdb_00004eup

The complex between TCR JKF6 and human Class I MHC HLA-A2 presenting the MART-1(27-35)(A27L) peptide

• PDB DOI: https://doi.org/10.2210/pdb4EUP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-04-25 Released: 2013-05-01 
• Deposition Author(s): Hossain, M., Baker, B.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.295 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Models: experimental

Literature

Structural description of how different MART-1 antigenic peptides influence JKF6 T cell receptor recognition

Hossain, M., Baker, B.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 189.68 kDa 
• Atom Count: 13,167 
• Modeled Residue Count: 1,633 
• Deposited Residue Count: 1,666 
• 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 D], D [auth A]	275	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 E], E [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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Melanoma antigen recognized by T-cells 1	C [auth F], F [auth C]	9	Homo sapiens	Mutation(s): 1
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
JKF6 alpha chain	G, H [auth I]	206	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
JKF6 beta chain	I [auth H], J	243	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free:  0.295 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.655	α = 90
b = 53.7	β = 112.46
c = 150.514	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Hossain, M., Baker, B.M.

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary