3AM8 | pdb_00003am8

Crystal Structure of a Human Major Histocompatibilty complex

• PDB DOI: https://doi.org/10.2210/pdb3AM8/pdb

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


• Deposited: 2010-08-18 Released: 2011-08-24 
• Deposition Author(s): Chacko, J., Clements, C., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structure of a Human Major Histocompatibility complex

Chacko, J., Clements, C., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 89.61 kDa 
• Atom Count: 6,427 
• Modeled Residue Count: 770 
• Deposited Residue Count: 770 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, alpha chain E	A, B	276	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P13747 (Homo sapiens) Explore P13747  Go to UniProtKB:  P13747
PHAROS:  P13747 GTEx:  ENSG00000204592

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	C, D	100	Homo sapiens	Mutation(s): 0
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 Glycoprotein	E, F	9	N/A	Mutation(s): 0
UniProt
Find proteins for Q0QI92 (Human cytomegalovirus) Explore Q0QI92  Go to UniProtKB:  Q0QI92

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.628	α = 90
b = 99.237	β = 92.72
c = 76.59	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-24 
Deposition Author(s): Chacko, J., Clements, C., Rossjohn, J.

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary