3P4O

Crystal Structure of H2-Kb in complex with the mutant NP205-LCMV-V3A epitope YTAKYPNL, an 8-mer modified peptide from the LCMV

• PDB DOI: https://doi.org/10.2210/pdb3P4O/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Mammarenavirus choriomeningitidis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-10-06 Released: 2011-10-12 
• Deposition Author(s): Gras, S., Guillonneau, C., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.275 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Starting Model: experimental

Literature

Crystal Structure of H2-Kb in complex with the mutant NP205-LCMV-V3A epitope YTAKYPNL, an 8-mer modified peptide from the LCMV

Gras, S., Guillonneau, 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: 89.64 kDa 
• Atom Count: 6,773 
• Modelled Residue Count: 769 
• Deposited Residue Count: 770 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-B alpha chain	A, D	278	Mus musculus	Mutation(s): 0  Gene Names: H2-K1, H2-K
UniProt
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, E	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
IMPC:  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NP205-LCMV epitope, YTAKYPNL	C, F	8	N/A	Mutation(s): 1  EC: 3.1.13
UniProt
Find proteins for Q91B91 (Mammarenavirus choriomeningitidis) Explore Q91B91  Go to UniProtKB:  Q91B91

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACE	G [auth E], H [auth E]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.275 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.75	α = 90
b = 85.05	β = 111.33
c = 89.18	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Gras, S., Guillonneau, C., Rossjohn, J.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description