4GBX

Crystal structure of an immune complex at pH 6.5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Crystal Structure of the HLA-DM-HLA-DR1 Complex Defines Mechanisms for Rapid Peptide Selection.

Pos, W., Sethi, D.K., Call, M.J., Schulze, M.S., Anders, A.K., Pyrdol, J., Wucherpfennig, K.W.

(2012) Cell 151: 1557-1568

  • DOI: 10.1016/j.cell.2012.11.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • HLA-DR molecules bind microbial peptides in an endosomal compartment and present them on the cell surface for CD4 T cell surveillance. HLA-DM plays a critical role in the endosomal peptide selection process. The structure of the HLA-DM-HLA-DR complex ...

    HLA-DR molecules bind microbial peptides in an endosomal compartment and present them on the cell surface for CD4 T cell surveillance. HLA-DM plays a critical role in the endosomal peptide selection process. The structure of the HLA-DM-HLA-DR complex shows major rearrangements of the HLA-DR peptide-binding groove. Flipping of a tryptophan away from the HLA-DR1 P1 pocket enables major conformational changes that position hydrophobic HLA-DR residues into the P1 pocket. These conformational changes accelerate peptide dissociation and stabilize the empty HLA-DR peptide-binding groove. Initially, incoming peptides have access to only part of the HLA-DR groove and need to compete with HLA-DR residues for access to the P2 site and the hydrophobic P1 pocket. This energetic barrier creates a rapid and stringent selection process for the highest-affinity binders. Insertion of peptide residues into the P2 and P1 sites reverses the conformational changes, terminating selection through DM dissociation.

    Organizational Affiliation: 

    Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DM alpha chain
C
203Homo sapiensMutation(s): 1 
Gene Names: HLA-DMA (DMA, RING6)
Find proteins for P28067 (Homo sapiens)
Go to Gene View: HLA-DMA
Go to UniProtKB:  P28067
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DM beta chain
D
199Homo sapiensMutation(s): 2 
Gene Names: HLA-DMB (DMB, RING7)
Find proteins for P28068 (Homo sapiens)
Go to Gene View: HLA-DMB
Go to UniProtKB:  P28068
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A
191Homo sapiensMutation(s): 1 
Gene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DRB1-1 beta chain
B
208Homo sapiensMutation(s): 1 
Gene Names: HLA-DRB1 (HLA-DRB2)
Find proteins for P01911 (Homo sapiens)
Go to Gene View: HLA-DRB1
Go to UniProtKB:  P01911
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
synthetic peptide
E
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.167α = 90.00
b = 126.032β = 90.00
c = 143.107γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
ADSCdata collection
PDB_EXTRACTdata extraction
PHENIXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description