7CIO | pdb_00007cio

Molecular interactions of cytoplasmic region of CTLA-4 with SH2 domains of PI3-kinase

• PDB DOI: https://doi.org/10.2210/pdb7CIO/pdb

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


• Deposited: 2020-07-08 Released: 2020-12-09 
• Deposition Author(s): Iiyama, M., Numoto, N., Ogawa, S., Kuroda, M., Morii, H., Abe, R., Ito, N., Oda, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Molecular interactions of the CTLA-4 cytoplasmic region with the phosphoinositide 3-kinase SH2 domains.

Iiyama, M., Numoto, N., Ogawa, S., Kuroda, M., Morii, H., Abe, R., Ito, N., Oda, M.

(2021) Mol Immunol 131: 51-59

• PubMed: 33386150 
• DOI: https://doi.org/10.1016/j.molimm.2020.12.002
• Primary Citation Related Structures: 
  7CIO


• PubMed Abstract: 
  

  During T-cell regulation, T-cell receptors and CD28 lead to signaling activation, while T-lymphocyte antigen 4 (CTLA-4) is known to lead to downregulation, similar to programmed cell death-1 (PD-1). In the cytoplasmic tails of CD28 and CTLA-4, phosphoinositide 3-kinase (PI3K) binds to the consensus sequence including phosphotyrosine via SH2 domains, N- and C-terminal SH2 domains (nSH2 and cSH2), of its regulatory subunit, p85. In this study, we determined the crystal structure of a CTLA-4-derived phosphopeptide in complex with a Cys-substituted mutant of cSH2, C656S/C659V/C670L, at a 1.1 Å resolution. Phosphotyrosine of the bound peptide is tightly accommodated by the residues Arg631, Arg649, Ser651, and Ser652, similar to the cSH2 wild-type recognition mode of CD28, as reported previously. Upon the Cys mutation, the cSH2 thermal stability increased while the CTLA-4 binding affinity slightly changed. The binding experiments also showed that the binding affinity of CTLA-4 by cSH2 was approximately two orders of magnitude lower than that of CD28. Similar to CD28 binding, the CTLA-4 binding affinity of nSH2 was lower than that of cSH2. The complex structure of nSH2 and CTLA-4 was modeled, and compared with the crystal structure of cSH2 mutant and CTLA-4. The difference in the binding affinity between CD28 and CTLA-4, along with the difference between nSH2 and cSH2, could be explained by the 3D structures, which would be closely correlated with the respective T-cell signaling.

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Organizational Affiliation: 
• Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan.
Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima Bunkyo-ku, Tokyo 113-8510, Japan.
Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan.
Laboratory of Bioinformatics, AI Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan.
Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-0074, Japan.
Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.15 kDa 
• Atom Count: 1,126 
• Modeled Residue Count: 117 
• Deposited Residue Count: 117 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase regulatory subunit alpha	A	109	Homo sapiens	Mutation(s): 3  Gene Names: PIK3R1, GRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens) Explore P27986  Go to UniProtKB:  P27986
PHAROS:  P27986 GTEx:  ENSG00000145675

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytotoxic T-lymphocyte protein 4	B	8	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P16410 (Homo sapiens) Explore P16410  Go to UniProtKB:  P16410
PHAROS:  P16410 GTEx:  ENSG00000163599

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.221	α = 90
b = 41.563	β = 90
c = 59.628	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Iiyama, M., Numoto, N., Ogawa, S., Kuroda, M., Morii, H., Abe, R., Ito, N., Oda, M.

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2021-03-17
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary