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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.251 (Depositor), 0.244 (DCC)
R-Value Work:
0.185 (Depositor), 0.182 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Structure of a Human Major Histocompatibility complex

Chacko, J., Clements, C., Rossjohn, J.

To be published.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13747
Sequence Annotations Expand
Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
UniProt Group	Q0QI92
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.251 (Depositor), 0.244 (DCC)
R-Value Work: 0.185 (Depositor), 0.182 (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

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Entry History

Deposition Data

Released Date: 2011-08-24

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.