2X2C | pdb_00002x2c

acetyl-CypA:cyclosporine complex

PDB DOI: https://doi.org/10.2210/pdb2X2C/pdb

Classification: ISOMERASE/IMMUNOSUPPRESSANT
Organism(s): Tolypocladium inflatum, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-01-12 Released: 2010-03-23
Deposition Author(s): Lammers, M., Neumann, H., Chin, J.W., James, L.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.264 (Depositor), 0.264 (DCC)
R-Value Work:
0.206 (Depositor), 0.211 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Acetylation Regulates Cyclophilin a Catalysis, Immunosuppression and HIV Isomerisation

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

(2010) Nat Chem Biol 6: 331

PubMed: 20364129 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 96.49 kDa
Atom Count: 7,267
Modeled Residue Count: 880
Deposited Residue Count: 880
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOSPORIN A	A [auth B], B [auth F], D [auth L], G [auth P], I [auth R]	11	Tolypocladium inflatum	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A	C [auth K], E [auth M], F [auth O], H [auth Q], J [auth S]	165	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62937
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 6 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA Query on ABA	A [auth B], B [auth F], D [auth L], G [auth P], I [auth R]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
BMT Query on BMT	A [auth B], B [auth F], D [auth L], G [auth P], I [auth R]	L-PEPTIDE LINKING	C₁₀ H₁₉ N O₃		THR
DAL Query on DAL	A [auth B], B [auth F], D [auth L], G [auth P], I [auth R]	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
MLE Query on MLE	A [auth B], B [auth F], D [auth L], G [auth P], I [auth R]	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
MVA Query on MVA	A [auth B], B [auth F], D [auth L], G [auth P], I [auth R]	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on SAR	A [auth B], B [auth F], D [auth L], G [auth P], I [auth R]	PEPTIDE LINKING	C₃ H₇ N O₂		GLY
ALY Query on ALY	C [auth K], E [auth M], F [auth O], H [auth Q], J [auth S]	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000142 Query on PRD_000142	A [auth B], B [auth F], D [auth L], G [auth P], I [auth R]	Cyclosporin A	Cyclic peptide / Immunosuppressant		Interactions Focus chain A [auth B] Focus chain B [auth F] Focus chain D [auth L] Focus chain G [auth P] Focus chain I [auth R] Interactions & Density Focus chain A [auth B] Focus chain B [auth F] Focus chain D [auth L] Focus chain G [auth P] Focus chain I [auth R]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.264 (Depositor), 0.264 (DCC)
R-Value Work: 0.206 (Depositor), 0.211 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.429	α = 90
b = 107.429	β = 90
c = 428.871	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
Version 1.2: 2011-10-26
Changes: Database references
Version 1.3: 2012-11-30
Changes: Other
Version 1.4: 2018-05-02
Changes: Advisory, Data collection
Version 1.5: 2025-04-09
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Structure summary