7DZM | pdb_00007dzm

Crystal Structure of the cross-restricted T18A TCR and HLAB8101 bound to HIV-1 Gag TL9 peptide

• PDB DOI: https://doi.org/10.2210/pdb7DZM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-25 Released: 2022-01-26 
• Deposition Author(s): Liu, Y., Yin, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Models: experimental

Literature

Cross-reactive TCR with alloreactivity for immunodominant HIV-1 epitope Gag TL9 with enhanced control of viral infection

Liu, Y., San, D., Yin, L.

(2021) bioRxiv 

• DOI: https://doi.org/10.1101/2021.06.06.447276

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 95.25 kDa 
• Atom Count: 7,079 
• Modeled Residue Count: 829 
• Deposited Residue Count: 835 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	278	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B
UniProt
Find proteins for I3ZN85 (Homo sapiens) Explore I3ZN85  Go to UniProtKB:  I3ZN85

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
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
Gag-Pol polyprotein	C	9	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
beta chain T18A TCR	D	241	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha chain T18A TCR	E	207	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.098	α = 90
b = 93.098	β = 90
c = 263.051	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-26 
Deposition Author(s): Liu, Y., Yin, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870728
National Natural Science Foundation of China (NSFC)	China	31470738

Revision History  

• Version 1.0: 2022-01-26
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary