Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 45.41 kDa 
• Atom Count: 3572 
• Residue Count: 381 
• Unique protein chains: 3

1LEG

Crystal Structure of H-2Kb bound to the dEV8 peptide

• DOI: 10.2210/pdb1LEG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2002-04-09 Released: 2002-06-19 
• Deposition Author(s): Luz, J.G., Huang, M., Garcia, K.C., Rudolph, M.G., Apostolopoulos, V., Teyton, L., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.241 
• R-Value Work: 0.217 

Literature

Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(beta) Interactions.

Luz, J.G., Huang, M., Garcia, K.C., Rudolph, M.G., Apostolopoulos, V., Teyton, L., Wilson, I.A.

(2002) J Exp Med 195: 1175-1186

• PubMed: 11994422 
• DOI: 10.1084/jem.20011644
• Primary Citation of Related Structures:  
  1LEG, 1LEK, 1MWA


• PubMed Abstract: 
  

The crystal structures of the 2C/H-2K(bm3)-dEV8 allogeneic complex at 2.4 A and H-2K(bm3)-dEV8 at 2.15 A, when compared with their syngeneic counterparts, elucidate structural changes that induce an alloresponse. The Asp77Ser mutation that imbues H-2K(bm3)-dEV8 with its alloreactive properties is located beneath the peptide and does not directly contact the T cell receptor (TCR). However, the buried mutation induces local rearrangement of the peptide itself to preserve hydrogen bonding interactions between the peptide and the alpha(1) 77 residue. The COOH terminus of the peptide main chain is tugged toward the alpha(1)-helix such that its presentation to the TCR is altered. These changes increase the stability of the allogeneic peptide-major histocompatibility complex (pMHC) complex and increase complementarity in the TCR-pMHC interface, placing greater emphasis on recognition of the pMHC by the TCR beta-chain, evinced by an increase in shape complementarity, buried surface area, and number of TCR-pMHC contacting residues. A nearly fourfold increase in the number of beta-chain-pMHC contacts is accompanied by a concomitant 64% increase in beta-chain-pMHC shape complementarity. Thus, the allogeneic mutation causes the same peptide to be presented differently, temporally and spatially, by the allogeneic and syngeneic MHCs.

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Organizational Affiliation: 

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, 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): 1  Gene Names: H2-K1, H2-K
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
NADH-ubiquinone oxidoreductase MLRQ subunit	P	8	N/A	Mutation(s): 0
Find proteins for Q62425 (Mus musculus) Explore Q62425  Go to UniProtKB:  Q62425

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation

Small Molecules

Ligands 2 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
PO4	A, B	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.241 
• R-Value Work: 0.217 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.687	α = 90
b = 87.686	β = 90
c = 45.213	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-04-09 
• Released Date: 2002-06-19 
Deposition Author(s): Luz, J.G., Huang, M., Garcia, K.C., Rudolph, M.G., Apostolopoulos, V., Teyton, L., Wilson, I.A.

Revision History 

• Version 1.0: 2002-06-19
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary