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 PQS (software)

Macromolecule Content

• Total Structure Weight: 45.72 kDa 
• Atom Count: 4130 
• Residue Count: 385 
• Unique protein chains: 3

1OGT

CRYSTAL STRUCTURE OF HLA-B*2705 COMPLEXED WITH THE VASOACTIVE INTESTINAL PEPTIDE TYPE 1 RECEPTOR (VIPR) PEPTIDE (RESIDUES 400-408)

• DOI: 10.2210/pdb1OGT/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-05-13 Released: 2004-01-29 
• Deposition Author(s): Hulsmeyer, M., Fiorillo, M.T., Bettosini, F., Sorrentino, R., Saenger, W., Ziegler, A., Uchanska-Ziegler, B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.178 
• R-Value Work: 0.128 
• R-Value Observed: 0.131 

Literature

Dual, HLA-B27 subtype-dependent conformation of a self-peptide.

Hulsmeyer, M., Fiorillo, M.T., Bettosini, F., Sorrentino, R., Saenger, W., Ziegler, A., Uchanska-Ziegler, B.

(2004) J Exp Med 199: 271-281

• PubMed: 14734527 
• DOI: 10.1084/jem.20031690
• Primary Citation of Related Structures:  
  1OF2, 1OGT


• PubMed Abstract: 
  

The products of the human leukocyte antigen subtypes HLA-B*2705 and HLA-B*2709 differ only in residue 116 (Asp vs. His) within the peptide binding groove but are differentially associated with the autoimmune disease ankylosing spondylitis (AS); HLA-B*2705 occurs in AS-patients, whereas HLA-B*2709 does not. The subtypes also generate differential T cell repertoires as exemplified by distinct T cell responses against the self-peptide pVIPR (RRKWRRWHL). The crystal structures described here show that pVIPR binds in an unprecedented dual conformation only to HLA-B*2705 molecules. In one binding mode, peptide pArg5 forms a salt bridge to Asp116, connected with drastically different interactions between peptide and heavy chain, contrasting with the second, conventional conformation, which is exclusively found in the case of B*2709. These subtype-dependent differences in pVIPR binding link the emergence of dissimilar T cell repertoires in individuals with HLA-B*2705 or HLA-B*2709 to the buried Asp116/His116 polymorphism and provide novel insights into peptide presentation by major histocompatibility antigens.

---

Related Citations: 

• Hla-B27 Subtypes Differentially Associated with Disease Exhibit Subtle Structural Alterations
  Hulsmeyer, M., Hillig, R.C., Volz, A., Ruhl, M., Schroder, W., Saenger, W., Ziegler, A., Uchanska-Ziegler, B.
  (2002) J Biol Chem 277: 47844

• The Three-Dimensional Structure of Hla-B27 at 2.1 A Resolution Suggests a General Mechanism for Tight Peptide Binding to Mhc
  Madden, D.R., Gorga, J.C., Strominger, J.L., Wiley, D.C.
  (1992) Cell 70: 1035

---

Organizational Affiliation: 

Institut für Kristallographie, Freie Universität Berlin, 14195 Berlin, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, HLAB
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
NIH Common Fund Data Resources
PHAROS:  P01889 GTEx:  ENSG00000234745

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
VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 1	C	9	Homo sapiens	Mutation(s): 0  Gene Names: VIPR1
Find proteins for P32241 (Homo sapiens) Explore P32241  Go to UniProtKB:  P32241
NIH Common Fund Data Resources
PHAROS:  P32241 GTEx:  ENSG00000114812

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B, C	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.178 
• R-Value Work: 0.128 
• R-Value Observed: 0.131 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.259	α = 90
b = 81.777	β = 107.61
c = 65.617	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-13 
• Released Date: 2004-01-29 
Deposition Author(s): Hulsmeyer, M., Fiorillo, M.T., Bettosini, F., Sorrentino, R., Saenger, W., Ziegler, A., Uchanska-Ziegler, B.

Revision History 

• Version 1.0: 2004-01-29
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2018-12-19
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 2.2: 2019-05-22
  Changes: Data collection, Experimental preparation