7NME | pdb_00007nme

Human MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR

• PDB DOI: https://doi.org/10.2210/pdb7NME/pdb

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


• Deposited: 2021-02-23 Released: 2022-09-07 
• Deposition Author(s): Rizkallah, P.J., Sewell, A.K., Cole, D.K., Wall, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.274 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7NMD 7NMF 7NMG

Literature

Human MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR

Rizkallahp, P.J., Sewell, A.K., Cole, D.K., Wall, A.

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: 94.08 kDa 
• Atom Count: 6,814 
• Modeled Residue Count: 816 
• Deposited Residue Count: 817 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for A0A5H2UYS3 (Homo sapiens) Explore A0A5H2UYS3  Go to UniProtKB:  A0A5H2UYS3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human MHC Class I, beta 2 microglobulin	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
GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU	C	9	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
4C6 Human T-cell Receptor, alpha Chain	D	192	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
4C6 Human T-cell Receptor, beta Chain	E	240	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	F [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.274 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.163	α = 90
b = 71.347	β = 90
c = 220.185	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
xia2	data reduction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-09-07 
Deposition Author(s): Rizkallah, P.J., Sewell, A.K., Cole, D.K., Wall, A.

Revision History  

• Version 1.0: 2022-09-07
  Type: Initial release
  
• Version 1.1: 2022-10-26
  Changes: Derived calculations
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary