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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.240 (Depositor), 0.237 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

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

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3ZN85
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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 Groups
UniProt Group	P04585
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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

Find similar proteins by:

| 3D Structure

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), 0.237 (DCC)
R-Value Work: 0.196 (Depositor), 0.196 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-26

Deposition Author(s):

Liu, Y.

Yin, L.

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 (Full details and data files)

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