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: 44.89 kDa 
• Atom Count: 3573 
• Modelled Residue Count: 383 
• Deposited 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
• Mutation(s): No 


• 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: 1.60 Å
• R-Value Free: 0.232 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 

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:  
  3BH8, 3BGM, 3BHB, 3BH9


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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) Explore P04439  Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
nonameric peptide from Serine/threonine-protein kinase D2	C	9	N/A	Mutation(s): 0
Find proteins for Q9BZL6 (Homo sapiens) Explore Q9BZL6  Go to UniProtKB:  Q9BZL6
NIH Common Fund Data Resources
PHAROS:  Q9BZL6 GTEx:  ENSG00000105287

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth B]	1,2-ETHANEDIOL 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: 1.60 Å
• R-Value Free: 0.232 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.8	α = 90
b = 54.8	β = 105
c = 75.8	γ = 90

Software Package:

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

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
  Changes: Version format compliance