Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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: 44.50 kDa 
• Atom Count: 3293 
• Residue Count: 381 
• Unique protein chains: 3

1RK0

Mhc Class I H-2Kb Heavy Chain Complexed With beta-2 Microglobulin and Herpes Simplex Virus Glycoprotein B peptide

• DOI: 10.2210/pdb1RK0/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2003-11-20 Released: 2004-12-14 
• Deposition Author(s): Miley, M.J., Messaoudi, I., Nikolich-Zugich, J., Fremont, D.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.238 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

Structural Basis for the Restoration of TCR Recognition of an MHC Allelic Variant by Peptide Secondary Anchor Substitution

Miley, M.J., Messaoudi, I., Metzner, B.M., Wu, Y., Nikolich-Zugich, J., Fremont, D.H.

(2004) J Exp Med 200: 1445-1454

• PubMed: 15557346 
• DOI: 10.1084/jem.20040217
• Primary Citation of Related Structures:  
  1RJZ, 1RJY, 1RK1, 1RK0


• PubMed Abstract: 
  

Major histocompatibility complex (MHC) class I variants H-2K(b) and H-2K(bm8) differ primarily in the B pocket of the peptide-binding groove, which serves to sequester the P2 secondary anchor residue. This polymorphism determines resistance to lethal herpes simplex virus (HSV-1) infection by modulating T cell responses to the immunodominant glycoprotein B(498-505) epitope, HSV8. We studied the molecular basis of these effects and confirmed that T cell receptors raised against K(b)-HSV8 cannot recognize H-2K(bm8)-HSV8. However, substitution of Ser(P2) to Glu(P2) (peptide H2E) reversed T cell receptor (TCR) recognition; H-2K(bm8)-H2E was recognized whereas H-2K(b)-H2E was not. Insight into the structural basis of this discrimination was obtained by determining the crystal structures of all four MHC class I molecules in complex with bound peptide (pMHCs). Surprisingly, we find no concerted pMHC surface differences that can explain the differential TCR recognition. However, a correlation is apparent between the recognition data and the underlying peptide-binding groove chemistry of the B pocket, revealing that secondary anchor residues can profoundly affect TCR engagement through mechanisms distinct from the alteration of the resting state conformation of the pMHC surface.

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Organizational Affiliation: 

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-B alpha chain	A	274	Mus musculus	Mutation(s): 0  Gene Names: H2-K, H2-K1
Find proteins for P01901 (Mus musculus) Explore P01901  Go to UniProtKB:  P01901

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC:  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein B	P	8	N/A	Mutation(s): 0
Find proteins for P06436 (Human herpesvirus 1 (strain F)) Explore P06436  Go to UniProtKB:  P06436

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.238 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.89	α = 90
b = 90.222	β = 90
c = 45.451	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-20 
• Released Date: 2004-12-14 
Deposition Author(s): Miley, M.J., Messaoudi, I., Nikolich-Zugich, J., Fremont, D.H.

Revision History 

• Version 1.0: 2004-12-14
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary