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- PDB-2rmc: Crystal structure of murine cyclophilin C complexed with immunosu... -

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Basic information

Entry
Database: PDB / ID: 2rmc
TitleCrystal structure of murine cyclophilin C complexed with immunosuppressive drug cyclosporin A
Components
  • CYCLOSPORIN A
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE C
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / 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 C
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.64 Å
AuthorsKe, H. / Zhao, Y. / Luo, F. / Weissman, I. / Friedman, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of Murine Cyclophilin C Complexed with Immunosuppressive Drug Cyclosporin A
Authors: Ke, H. / Zhao, Y. / Luo, F. / Weissman, I. / Friedman, J.
History
DepositionJan 7, 1994Processing site: BNL
Revision 1.0Feb 14, 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: Advisory / Atomic model ...Advisory / 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 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / struct_conn
Item: _atom_site.Cartn_x / _atom_sites.fract_transf_vector[1] ..._atom_site.Cartn_x / _atom_sites.fract_transf_vector[1] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx_vector[1] / _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
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Dec 6, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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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 C
B: CYCLOSPORIN A
C: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE C
D: CYCLOSPORIN A
E: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE C
F: CYCLOSPORIN A
G: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE C
H: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)84,6498
Polymers84,6498
Non-polymers00
Water7,224401
1
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE C
B: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)21,1622
Polymers21,1622
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area998 Å2
ΔGint-2 kcal/mol
Surface area8428 Å2
MethodPISA
2
C: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE C
D: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)21,1622
Polymers21,1622
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area993 Å2
ΔGint-2 kcal/mol
Surface area8479 Å2
MethodPISA
3
E: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE C
F: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)21,1622
Polymers21,1622
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area984 Å2
ΔGint-2 kcal/mol
Surface area8553 Å2
MethodPISA
4
G: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE C
H: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)21,1622
Polymers21,1622
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area994 Å2
ΔGint-2 kcal/mol
Surface area8459 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.300, 74.000, 97.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUE ALA 8 IN CHAINS B, D, F, AND H IS A D-ALANINE.

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Components

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


Mass: 19941.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / References: UniProt: P30412, peptidylprolyl isomerase
#2: Protein/peptide
CYCLOSPORIN A / CICLOSPORIN / CICLOSPORINE


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 4 / 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.: 401 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / 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
614 %(w/v)PEG335012
76 %(v/v)ethanol12
82 %(v/v)isopropanol12
90.2 Mammonium sulfate12
100.01 mMCsA12

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.64 Å / Num. obs: 73850 / Num. measured all: 139812 / Rmerge(I) obs: 0.04

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.64→6 Å
Details: THE SPACE GROUP IS P21 WITH THE ORIGIN AT 1/4 OF X SO THAT THE SYMMETRY IS (X,Y,Z) AND (1/2-X, 1/2+Y,-X).
RfactorNum. reflection
Rwork0.197 -
obs0.197 72159
Refinement stepCycle: LAST / Resolution: 1.64→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5928 0 0 401 6329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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
Rfactor obs: 0.197 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.68

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