Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 44.77 kDa 
• Atom Count: 3611 
• Residue Count: 383 
• Unique protein chains: 3

4JQV

HLA-B*18:01 in complex with Epstein-Barr virus BZLF1-derived peptide (residues 173-180)

• DOI: 10.2210/pdb4JQV/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human gammaherpesvirus 4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-20 Released: 2013-06-26 
• Deposition Author(s): Theodossis, A., Welland, A., Gras, S., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.214 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

HLA Peptide Length Preferences Control CD8+ T Cell Responses.

Rist, M.J., Theodossis, A., Croft, N.P., Neller, M.A., Welland, A., Chen, Z., Sullivan, L.C., Burrows, J.M., Miles, J.J., Brennan, R.M., Gras, S., Khanna, R., Brooks, A.G., McCluskey, J., Purcell, A.W., Rossjohn, J., Burrows, S.R.

(2013) J Immunol 191: 561-571

• PubMed: 23749632 
• DOI: 10.4049/jimmunol.1300292
• Primary Citation of Related Structures:  
  4JQV, 4JQX


• PubMed Abstract: 
  

Class I HLAs generally present peptides of 8-10 aa in length, although it is unclear whether peptide length preferences are affected by HLA polymorphism. In this study, we investigated the CD8(+) T cell response to the BZLF1 Ag of EBV, which includes overlapping sequences of different size that nevertheless conform to the binding motif of the large and abundant HLA-B*44 supertype. Whereas HLA-B*18:01(+) individuals responded strongly and exclusively to the octamer peptide (173)SELEIKRY(180), HLA-B*44:03(+) individuals responded to the atypically large dodecamer peptide (169)EECDSELEIKRY(180), which encompasses the octamer peptide. Moreover, the octamer peptide bound more stably to HLA-B*18:01 than did the dodecamer peptide, whereas, conversely, HLA-B*44:03 bound only the longer peptide. Furthermore, crystal structures of these viral peptide-HLA complexes showed that the Ag-binding cleft of HLA-B*18:01 was more ideally suited to bind shorter peptides, whereas HLA-B*44:03 exhibited characteristics that favored the presentation of longer peptides. Mass spectrometric identification of > 1000 naturally presented ligands revealed that HLA-B*18:01 was more biased toward presenting shorter peptides than was HLA-B*44:03. Collectively, these data highlight a mechanism through which polymorphism within an HLA class I supertype can diversify determinant selection and immune responses by varying peptide length preferences.

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Organizational Affiliation: 

Centre for Immunotherapy and 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-18 alpha chain	A	278	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, HLAB
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
NIH Common Fund Data Resources
PHAROS  P01889 GTEx  ENSG00000234745

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	C	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769 GTEx  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Trans-activator protein BZLF1	B	8	Human gammaherpesvirus 4	Mutation(s): 0  Gene Names: BZLF1
Find proteins for Q3KSS8 (Epstein-Barr virus (strain GD1)) Explore Q3KSS8  Go to UniProtKB:  Q3KSS8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.214 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.848	α = 90
b = 81.251	β = 90
c = 110.892	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-20 
• Released Date: 2013-06-26 
Deposition Author(s): Theodossis, A., Welland, A., Gras, S., Rossjohn, J.

Revision History 

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references