5WET

Crystal Structure of H2-Dd with disulfide-linked 6mer peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a TAPBPR-MHC I complex reveals the mechanism of peptide editing in antigen presentation.

Jiang, J.Natarajan, K.Boyd, L.F.Morozov, G.I.Mage, M.G.Margulies, D.H.

(2017) Science 358: 1064-1068

  • DOI: 10.1126/science.aao5154
  • Primary Citation of Related Structures:  
    5WET, 5WES, 5WEU, 5WER

  • PubMed Abstract: 
  • Central to CD8 + T cell-mediated immunity is the recognition of peptide-major histocompatibility complex class I (p-MHC I) proteins displayed by antigen-presenting cells. Chaperone-mediated loading of high-affinity peptides onto MHC I is ...

    Central to CD8 + T cell-mediated immunity is the recognition of peptide-major histocompatibility complex class I (p-MHC I) proteins displayed by antigen-presenting cells. Chaperone-mediated loading of high-affinity peptides onto MHC I is a key step in the MHC I antigen presentation pathway. However, the structure of MHC I with a chaperone that facilitates peptide loading has not been determined. We report the crystal structure of MHC I in complex with the peptide editor TAPBPR (TAP-binding protein-related), a tapasin homolog. TAPBPR remodels the peptide-binding groove of MHC I, resulting in the release of low-affinity peptide. Changes include groove relaxation, modifications of key binding pockets, and domain adjustments. This structure captures a peptide-receptive state of MHC I and provides insights into the mechanism of peptide editing by TAPBPR and, by analogy, tapasin.


    Organizational Affiliation

    Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. dhm@nih.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-D alpha chainA277Mus musculusMutation(s): 1 
Gene Names: H2-D1
Find proteins for P01900 (Mus musculus)
Explore P01900 
Go to UniProtKB:  P01900
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB99Mus musculusMutation(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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Surface protein gp120P6Human immunodeficiency virus type 1 (BRU ISOLATE)Mutation(s): 1 
Gene Names: env
Find proteins for P03377 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03377 
Go to UniProtKB:  P03377
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LEU
Query on LEU

Download CCD File 
A
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
GLY
Query on GLY

Download CCD File 
A
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.324α = 90
b = 63.171β = 106.46
c = 91.558γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Database references
  • Version 1.2: 2017-12-13
    Changes: Database references