Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.01 kDa 
• Atom Count: 3754 
• Modelled Residue Count: 385 
• Deposited Residue Count: 385 
• Unique protein chains: 3

3VCL

Crystal Structure of HLA-B7 with the HCMV pp65 peptide RPHERNGFTVL

• PDB DOI: 10.2210/pdb3VCL/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human betaherpesvirus 5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-04 Released: 2012-11-21 
• Deposition Author(s): Petersen, J., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.217 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

The impact of a large and frequent deletion in the human TCR beta locus on antiviral immunity

Brennan, R.M., Petersen, J., Neller, M.A., Miles, J.J., Burrows, J.M., Smith, C., McCluskey, J., Khanna, R., Rossjohn, J., Burrows, S.R.

(2012) J Immunol 188: 2742-2748

• PubMed: 22323539 
• DOI: 10.4049/jimmunol.1102675
• Primary Citation of Related Structures:  
  3VCL


• PubMed Abstract: 
  

The TCR plays a critical role in recognizing intracellular pathogens and initiating pathways leading to the destruction of infected cells by the immune system. Although genetic variability is known to greatly impact on the human immune system and the outcome of infection, the influence of sequence variation leading to the inactivation or deletion of TCR gene segments is unknown. To investigate this issue, we examined the CD8(+) T cell response to an HLA-B7-restricted epitope ((265)RPHERNGFTVL(275)) from the pp65 Ag of human CMV that was highly biased and frequently dominated by a public TCR β-chain encoded by the variable gene segment TRBV4-3. Approximately 40% of humans lack T cells expressing TRBV4-3 because of a 21.5-kb insertion/deletion polymorphism, but these individuals remain responsive to this epitope, using a diverse T cell repertoire characterized by private TCR usage. Although most residues within the bulged 11-mer peptide were accessible for TCR contact, the public and private TCRs showed distinct patterns of sensitivity to amino acid substitution at different positions within the peptide, thereby suggesting that the repertoire diversity generated in the absence of the dominant public TRBV4-3(+) TCR could lead to better protection from viral escape mutation. Thus, variation in the size of the TRBV repertoire clearly contributes toward interindividual variability in immune responses and is presumably maintained in many ethnic groups to enhance the diversity of Ag-specific T cell responses.

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Organizational Affiliation: 

Australian Centre for Vaccine Development, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B-7 alpha chain	A	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, HLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
PHAROS:  P01889 GTEx:  ENSG00000234745

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	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
peptide from Tegument protein pp65	C	11	Human betaherpesvirus 5	Mutation(s): 0
UniProt
Find proteins for Q6SW59 (Human cytomegalovirus (strain Merlin)) Explore Q6SW59  Go to UniProtKB:  Q6SW59

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	D [auth A], E [auth A], J [auth B], K [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.217 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.786	α = 90
b = 65.786	β = 90
c = 237.107	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-04 
• Released Date: 2012-11-21 
Deposition Author(s): Petersen, J., Rossjohn, J.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release