7NMG

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

• PDB DOI: https://doi.org/10.2210/pdb7NMG/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: 2.48 Å
• R-Value Free: 0.271 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Re-refinement Note

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

Literature

Human MHC Class I, A24 Allele presenting LWM, 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: 94.48 kDa 
• Atom Count: 6,763 
• Modelled Residue Count: 817 
• 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
Diabetes epitope LWMRLLPLL	C	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308 GTEx:  ENSG00000254647

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

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Human 4C6 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
EPE	G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4	F [auth A], K [auth C], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO (Subject of Investigation/LOI)	H [auth B], I [auth B], J [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.271 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.32	α = 90
b = 72.13	β = 90
c = 230.65	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: 2024-01-31
  Changes: Data collection, Refinement description