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 4HS3 | pdb_00004hs3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.239 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1242/jcs.145334
  • Primary Citation 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.


  • Organizational Affiliation: 
    • Molecular Life Science Center, Jacobs University Bremen, 28759 Bremen, Germany.

Macromolecule Content 

  • Total Structure Weight: 44.68 kDa 
  • Atom Count: 3,585 
  • Modeled Residue Count: 383 
  • Deposited Residue Count: 383 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, K-B alpha chain276Mus musculusMutation(s): 2 
Gene Names: H2-K1, H2-K
UniProt
Find proteins for P01901 (Mus musculus)
Explore P01901 
Go to UniProtKB:  P01901
Entity Groups
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UniProt GroupP01901
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Mus musculusMutation(s): 1 
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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01887
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein8Mammarenavirus choriomeningitidisMutation(s): 1 
UniProt
Find proteins for Q9WKU1 (Mammarenavirus choriomeningitidis)
Explore Q9WKU1 
Go to UniProtKB:  Q9WKU1
Entity Groups
UniProt GroupQ9WKU1
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.239 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.59α = 90
b = 90.57β = 90
c = 137.37γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary