3MRF | pdb_00003mrf

Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288 nonapeptide T4P variant

• PDB DOI: https://doi.org/10.2210/pdb3MRF/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, human gammaherpesvirus 4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-04-29 Released: 2011-05-25 
• Deposition Author(s): Trudel, E., Gras, S., Chouquet, A., Debeaupuis, E., Echasserieau, K., Saulquin, X., Bonneville, M., Housset, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.257 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288 nonapeptide T4P variant

Trudel, E., Gras, S., Chouquet, A., Debeaupuis, E., Echasserieau, K., Saulquin, X., Bonneville, M., Housset, D.

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: 46.8 kDa 
• Atom Count: 3,372 
• Modeled Residue Count: 383 
• Deposited Residue Count: 402 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	A	293	Homo sapiens	Mutation(s): 1  Gene Names: HLA, HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, BETA-2 MICROGLUBULIN, 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
9-meric peptide from mRNA export factor EB2	C [auth P]	9	human gammaherpesvirus 4	Mutation(s): 1
UniProt
Find proteins for Q3KSU1 (Epstein-Barr virus (strain GD1)) Explore Q3KSU1  Go to UniProtKB:  Q3KSU1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.257 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.622	α = 90
b = 79.392	β = 112.02
c = 55.661	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Trudel, E., Gras, S., Chouquet, A., Debeaupuis, E., Echasserieau, K., Saulquin, X., Bonneville, M., Housset, D.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Data collection
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary