3SPV | pdb_00003spv

Crystal structure of a peptide-HLA complex

• PDB DOI: https://doi.org/10.2210/pdb3SPV/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human herpesvirus 4 strain B95-8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-04 Released: 2012-07-04 
• Deposition Author(s): Gras, S., Rossjohn, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.219 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a peptide-HLA complex

Gras, S., Rossjohn, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content 

• Total Structure Weight: 44.82 kDa 
• Atom Count: 4,055 
• Modeled Residue Count: 383 
• Deposited Residue Count: 383 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B-8 alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B
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
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 Trans-activator protein BZLF1	C	8	Human herpesvirus 4 strain B95-8	Mutation(s): 0
UniProt
Find proteins for P03206 (Epstein-Barr virus (strain B95-8)) Explore P03206  Go to UniProtKB:  P03206

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.219 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.56	α = 90
b = 81.46	β = 90
c = 110.02	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-04 
Deposition Author(s): Gras, S., Rossjohn, J.

Revision History  

• Version 1.0: 2012-07-04
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary