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- PDB-2rma: Crystal structures of cyclophilin A complexed with cyclosporin A ... -

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Basic information

Entry
Database: PDB / ID: 2rma
TitleCrystal structures of cyclophilin A complexed with cyclosporin A and N-methyl-4-[(E)-2-butenyl]-4,4-dimethylthreonine cyclosporin A
Components
  • CYCLOSPORIN A
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / protein peptidyl-prolyl isomerization / Basigin interactions / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / negative regulation of protein phosphorylation / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / Calcineurin activates NFAT / activation of protein kinase B activity / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Assembly Of The HIV Virion / positive regulation of protein secretion / Budding and maturation of HIV virion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of NF-kappaB transcription factor activity / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / integrin binding / positive regulation of protein phosphorylation / neuron differentiation / unfolded protein binding / Platelet degranulation / protein folding / cellular response to oxidative stress / vesicle / secretory granule lumen / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cyclosporin A / : / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsKe, H. / Mayrose, D.
CitationJournal: Structure / Year: 1994
Title: Crystal Structures of Cyclophilin a Complexed with Cyclosporin a and N-Methyl-4-[(E)-2-Butenyl]-4,4-Dimethylthreonine Cyclosporin A.
Authors: Ke, H. / Mayrose, D. / Belshaw, P.J. / Alberg, D.G. / Schreiber, S.L. / Chang, Z.Y. / Etzkorn, F.A. / Ho, S. / Walsh, C.T.
History
DepositionJan 7, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Nov 1, 2017Group: Derived calculations / Other / Category: pdbx_database_status / pdbx_struct_assembly
Item: _pdbx_database_status.process_site / _pdbx_struct_assembly.method_details
Revision 1.6Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
B: CYCLOSPORIN A
C: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
D: CYCLOSPORIN A
E: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
F: CYCLOSPORIN A
G: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
H: CYCLOSPORIN A
I: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
J: CYCLOSPORIN A
K: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
L: CYCLOSPORIN A
M: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
N: CYCLOSPORIN A
O: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
P: CYCLOSPORIN A
Q: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
R: CYCLOSPORIN A
S: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
T: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)192,57120
Polymers192,57120
Non-polymers00
Water11,385632
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27380 Å2
ΔGint-170.2 kcal/mol
Surface area58960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.600, 160.900, 95.300
Angle α, β, γ (deg.)90.00, 90.60, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUE ALA 8 IN CHAINS B, D, F, H, J, L, N, P, R, T IS A D-ALANINE.

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Components

#1: Protein
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / PPIASE / ROTAMASE / CYCLOPHILIN A


Mass: 18036.504 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: CYCLOPHILIN A / References: UniProt: P62937, peptidylprolyl isomerase
#2: Protein/peptide
CYCLOSPORIN A / CICLOSPORIN / CICLOSPORINE


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 10 / Source method: obtained synthetically
Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.
Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, Cyclosporin A
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113 mg/mlcomplex11
220 mMTris12
32 mMdithiothreitol12
42 mMEDTA12
50.5 mM12NaN3
69 %PEG335012
710 %ethanol12
82 %isopropanol12
90.3 Mammonium sulfate12
100.1 mMCsA12

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.17 / Rfactor obs: 0.17 / Highest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13510 0 0 632 14142
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 6 Å / Num. reflection obs: 100595 / Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.68

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