1O80 | pdb_00001o80

Crystal structure of IP-10 H-Form

• PDB DOI: https://doi.org/10.2210/pdb1O80/pdb

• Classification: CHEMOKINE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2002-11-20 Released: 2003-05-08 
• Deposition Author(s): Swaminathan, G.J., Holloway, D.E., Papageorgiou, A.C., Acharya, K.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.298 (Depositor) 
• R-Value Work: 
  0.264 (Depositor) 
• R-Value Observed: 
  0.264 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of Oligomeric Forms of the Ip-10/Cxcl10 Chemokine

Swaminathan, G.J., Holloway, D.E., Colvin, R.A., Campanella, G.K., Papageorgiou, A.C., Luster, A.D., Acharya, K.R.

(2003) Structure 11: 521

• PubMed: 12737818 
• DOI: https://doi.org/10.1016/s0969-2126(03)00070-4
• Primary Citation Related Structures: 
  1O7Y, 1O7Z, 1O80


• PubMed Abstract: 
  

  We have determined the structure of wild-type IP-10 from three crystal forms. The crystals provide eight separate models of the IP-10 chain, all differing substantially from a monomeric IP-10 variant examined previously by NMR spectroscopy. In each crystal form, IP-10 chains form conventional beta sheet dimers, which, in turn, form a distinct tetrameric assembly. The M form tetramer is reminiscent of platelet factor 4, whereas the T and H forms feature a novel twelve-stranded beta sheet. Analytical ultracentrifugation indicates that, in free solution, IP-10 exists in a monomer-dimer equilibrium with a dissociation constant of 9 microM. We propose that the tetrameric structures may represent species promoted by the binding of glycosaminoglycans. The binding sites for several IP-10-neutralizing mAbs have also been mapped.

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Organizational Affiliation: 
• Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 17.27 kDa 
• Atom Count: 1,189 
• Modeled Residue Count: 147 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SMALL INDUCIBLE CYTOKINE B10	A, B	77	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02778 (Homo sapiens) Explore P02778  Go to UniProtKB:  P02778
PHAROS:  P02778 GTEx:  ENSG00000169245

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.298 (Depositor) 
• R-Value Work:  0.264 (Depositor) 
• R-Value Observed: 0.264 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.56	α = 90
b = 84.56	β = 90
c = 116.967	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-08 
Deposition Author(s): Swaminathan, G.J., Holloway, D.E., Papageorgiou, A.C., Acharya, K.R.

Revision History  

• Version 1.0: 2003-05-08
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary