2X25 | pdb_00002x25

Free acetyl-CypA orthorhombic form

• PDB DOI: https://doi.org/10.2210/pdb2X25/pdb

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


• Deposited: 2010-01-11 Released: 2010-03-23 
• Deposition Author(s): Lammers, M., Neumann, H., Chin, J.W., James, L.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.156 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Literature

Acetylation Regulates Cyclophilin a Catalysis, Immunosuppression and HIV Isomerization.

Lammers, M., Neumann, H., Chin, J.W., James, L.C.

(2010) Nat Chem Biol 6: 331

• PubMed: 20364129 
• DOI: https://doi.org/10.1038/nchembio.342
• Primary Citation Related Structures: 
  2X25, 2X2A, 2X2C, 2X2D


• PubMed Abstract: 
  

  Cyclophilin A (CypA) is a ubiquitous cis-trans prolyl isomerase with key roles in immunity and viral infection. CypA suppresses T-cell activation through cyclosporine complexation and is required for effective HIV-1 replication in host cells. We show that CypA is acetylated in diverse human cell lines and use a synthetically evolved acetyllysyl-tRNA synthetase/tRNA(CUA) pair to produce recombinant acetylated CypA in Escherichia coli. We determined atomic-resolution structures of acetylated CypA and its complexes with cyclosporine and HIV-1 capsid. Acetylation markedly inhibited CypA catalysis of cis to trans isomerization and stabilized cis rather than trans forms of the HIV-1 capsid. Furthermore, CypA acetylation antagonized the immunosuppressive effects of cyclosporine by inhibiting the sequential steps of cyclosporine binding and calcineurin inhibition. Our results reveal that acetylation regulates key functions of CypA in immunity and viral infection and provide a general set of mechanisms by which acetylation modulates interactions to regulate cell function.

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Organizational Affiliation: 
• Medical Research Council Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 18.64 kDa 
• Atom Count: 1,744 
• Modeled Residue Count: 168 
• Deposited Residue Count: 169 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A	A [auth B]	169	Homo sapiens	Mutation(s): 0  EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens) Explore P62937  Go to UniProtKB:  P62937
PHAROS:  P62937 GTEx:  ENSG00000196262

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	A [auth B]	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.156 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.222	α = 90
b = 52.404	β = 90
c = 89.236	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Lammers, M., Neumann, H., Chin, J.W., James, L.C.

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-06-09
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary