Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.68 kDa 
• Atom Count: 3585 
• Residue Count: 383 
• Unique protein chains: 3

4HS3

Crystal structure of H-2Kb with a disulfide stabilized F pocket in complex with the LCMV derived peptide GP34

• DOI: 10.2210/pdb4HS3/pdb

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


• Deposited: 2012-10-29 Released: 2014-05-07 
• Deposition Author(s): Uchtenhagen, H., Boulanger, B., Hein, Z., Abualrous, E.T., Zacharias, M., Werner, J., Elliott, T., Springer, S., Achour, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Literature

Peptide-independent stabilization of MHC class I molecules breaches cellular quality control.

Hein, Z., Uchtenhagen, H., Abualrous, E.T., Saini, S.K., Janen, L., Van Hateren, A., Wiek, C., Hanenberg, H., Momburg, F., Achour, A., Elliott, T., Springer, S., Boulanger, D.

(2014) J Cell Sci 127: 2885-2897

• PubMed: 24806963 
• DOI: 10.1242/jcs.145334
• Primary Citation of Related Structures:  
  4HS3


• PubMed Abstract: 
  

The intracellular trafficking of major histocompatibility complex class I (MHC-I) proteins is directed by three quality control mechanisms that test for their structural integrity, which is correlated to the binding of high-affinity antigenic peptide ligands. To investigate which molecular features of MHC-I these quality control mechanisms detect, we have followed the hypothesis that suboptimally loaded MHC-I molecules are characterized by their conformational mobility in the F-pocket region of the peptide-binding site. We have created a novel variant of an MHC-I protein, K(b)-Y84C, in which two α-helices in this region are linked by a disulfide bond that mimics the conformational and dynamic effects of bound high-affinity peptide. K(b)-Y84C shows a remarkable increase in the binding affinity to its light chain, beta-2 microglobulin (β2m), and bypasses all three cellular quality control steps. Our data demonstrate (1) that coupling between peptide and β2m binding to the MHC-I heavy chain is mediated by conformational dynamics; (2) that the folded conformation of MHC-I, supported by β2m, plays a decisive role in passing the ER-to-cell-surface transport quality controls; and (3) that β2m association is also tested by the cell surface quality control that leads to MHC-I endocytosis.

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Organizational Affiliation: 

Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, Hampshire SO16 6YD, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-B alpha chain	A	276	Mus musculus	Mutation(s): 2  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): 1  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
Envelope glycoprotein	C	8	Lymphocytic choriomeningitis mammarenavirus	Mutation(s): 1  Gene Names: Gp-C
Find proteins for Q9WKU1 (Lymphocytic choriomeningitis mammarenavirus) Explore Q9WKU1  Go to UniProtKB:  Q9WKU1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	B	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.59	α = 90
b = 90.57	β = 90
c = 137.37	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-29 
• Released Date: 2014-05-07 
Deposition Author(s): Uchtenhagen, H., Boulanger, B., Hein, Z., Abualrous, E.T., Zacharias, M., Werner, J., Elliott, T., Springer, S., Achour, A.

Revision History 

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2014-05-21
  Changes: Database references
• Version 1.2: 2014-07-16
  Changes: Database references