2X44

Structure of a strand-swapped dimeric form of CTLA-4

• PDB DOI: https://doi.org/10.2210/pdb2X44/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-01-28 Released: 2010-04-07 
• Deposition Author(s): Sonnen, A.F.-P., Yu, C., Evans, E.J., Stuart, D.I., Davis, S.J., Gilbert, R.J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.245 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

Domain Metastability: A Molecular Basis for Immunoglobulin Deposition?

Sonnen, A.F., Yu, C., Evans, E.J., Stuart, D.I., Davis, S.J., Gilbert, R.J.C.

(2010) J Mol Biol 399: 207

• PubMed: 20394753 
• DOI: https://doi.org/10.1016/j.jmb.2010.04.011
• Primary Citation of Related Structures:  
  2X44


• PubMed Abstract: 
  

  We present the crystal structure of an immunoglobulin light-chain-like domain, CTLA-4, as a strand-swapped dimer displaying cis-trans proline isomerisation and native-like hydrogen bonding. We also show that CTLA-4 can form amyloid-like fibres and amorphous deposits explainable by the same strand swapping. Our results suggest a molecular basis for the pathological aggregation of immunoglobulin domains and why amyloid-like fibres are more often composed of homologous rather than heterologous subunits.

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Organizational Affiliation: 

Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. [e-mail]

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 PISA (software)

Macromolecule Content

• Total Structure Weight: 14.09 kDa 
• Atom Count: 964 
• Modelled Residue Count: 121 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOTOXIC T-LYMPHOCYTE PROTEIN 4	A [auth D]	131	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P16410 (Homo sapiens) Explore P16410  Go to UniProtKB:  P16410
PHAROS:  P16410 GTEx:  ENSG00000163599

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.245 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.951	α = 90
b = 42.951	β = 90
c = 140.101	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-07 
Deposition Author(s): Sonnen, A.F.-P., Yu, C., Evans, E.J., Stuart, D.I., Davis, S.J., Gilbert, R.J.C.

Revision History  

• Version 1.0: 2010-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-08-10
  Changes: Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary