Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 44893.79 
• Atom Count: 3173 
• Residue Count: 383 
• Unique protein chains: 3

3BGM

Crystal Structure of PKD2 Phosphopeptide Bound to Human Class I MHC HLA-A2

• DOI: 10.2210/pdb3BGM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2007-11-27 Released: 2008-10-21 
• Deposition Author(s): Mohammed, F., Cobbold, M., Zarling, A.L., Salim, M., Barrett-Wilt, G.A., Shabanowitz, J., Hunt, D.F., Engelhard, V.H., Willcox, B.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.232 
• R-Value Work: 0.202 

Literature

Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self

Mohammed, F., Cobbold, M., Zarling, A.L., Salim, M., Barrett-Wilt, G.A., Shabanowitz, J., Hunt, D.F., Engelhard, V.H., Willcox, B.E.

(2008) Nat.Immunol. 9: 1236-1243

• PubMed: 18836451 
• DOI: 10.1038/ni.1660
• Primary Citation of Related Structures:  
  3BHB, 3BH9, 3BH8


• PubMed Abstract: 
  

Protein phosphorylation generates a source of phosphopeptides that are presented by major histocompatibility complex class I molecules and recognized by T cells. As deregulated phosphorylation is a hallmark of malignant transformation, the differential display of phosphopeptides on cancer cells provides an immunological signature of 'transformed self'. Here we demonstrate that phosphorylation can considerably increase peptide binding affinity for HLA-A2. To understand this, we solved crystal structures of four phosphopeptide-HLA-A2 complexes. These identified a novel peptide-binding motif centered on a solvent-exposed phosphate anchor. Our findings indicate that deregulated phosphorylation can create neoantigens by promoting binding to major histocompatibility complex molecules or by affecting the antigenic identity of presented epitopes. These results highlight the potential of phosphopeptides as novel targets for cancer immunotherapy.

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Organizational Affiliation: 

Cancer Research UK Institute for Cancer Studies, School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA class I histocompatibility antigen, A-2 alpha chain	A	274	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A (HLAA)
Find proteins for P04439 (Homo sapiens) Go to Gene View: HLA-A Go to UniProtKB:  P04439

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for P61769 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  P61769

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
nonameric peptide from Serine/threonine-protein kinase D2	C	9	Homo sapiens	Mutation(s): 0  Gene Names: PRKD2 (PKD2) EC: 2.7.11.13
Find proteins for Q9BZL6 (Homo sapiens) Go to Gene View: PRKD2 Go to UniProtKB:  Q9BZL6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A, B	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	C	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.232 
• R-Value Work: 0.202 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 117.800	α = 90.00
b = 54.800	β = 105.00
c = 75.800	γ = 90.00

Software Package:

Software Name	Purpose
XSCALE	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-27 
• Released Date: 2008-10-21 
• Deposition Author(s): Mohammed, F., Cobbold, M., Zarling, A.L., Salim, M., Barrett-Wilt, G.A., Shabanowitz, J., Hunt, D.F., Engelhard, V.H., Willcox, B.E.

Revision History 

• Version 1.0: 2008-10-21
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance