3DTX

Crystal structure of HLA-B*2705 complexed with the double citrullinated vasoactive intestinal peptide type 1 receptor (VIPR) peptide (residues 400-408)

• PDB DOI: https://doi.org/10.2210/pdb3DTX/pdb

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


• Deposited: 2008-07-16 Released: 2009-05-05 
• Deposition Author(s): Beltrami, A., Gabdulkhakov, A., Rossmann, M., Ziegler, A., Uchanska-Ziegler, B., Saenger, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.262 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

Starting Model: experimental

Literature

Citrullination-and mhc polymorphism-dependent conformational changes of a self peptide

Beltrami, A., Gabdulkhakov, A., Rossmann, M., Ziegler, A., Uchanska-Ziegler, B., Saenger, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.21 kDa 
• Atom Count: 3,470 
• Modelled Residue Count: 385 
• Deposited Residue Count: 385 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen (Fragment)	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B
UniProt
Find proteins for A3F718 (Homo sapiens) Explore A3F718  Go to UniProtKB:  A3F718

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
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Double citrullinated vasoactive intestinal polypeptide receptor	C	9	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P32241 (Homo sapiens) Explore P32241  Go to UniProtKB:  P32241
PHAROS:  P32241 GTEx:  ENSG00000114812

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CIR	C	L-PEPTIDE LINKING	C6 H13 N3 O3		ARG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.262 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.842	α = 90
b = 81.931	β = 108.88
c = 65.771	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Beltrami, A., Gabdulkhakov, A., Rossmann, M., Ziegler, A., Uchanska-Ziegler, B., Saenger, W.

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-10-12
  Changes: Derived calculations
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-12-27
  Changes: Derived calculations
• Version 2.2: 2024-11-06
  Changes: Structure summary