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- PDB-1cwk: HUMAN CYCLOPHILIN A COMPLEXED WITH 1-(6,7-DIHYDRO)MEBMT 2-VAL 3-D... -

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Basic information

Entry
Database: PDB / ID: 1cwk
TitleHUMAN CYCLOPHILIN A COMPLEXED WITH 1-(6,7-DIHYDRO)MEBMT 2-VAL 3-D-(2-S-METHYL)SARCOSINE CYCLOSPORIN
Components
  • CYCLOSPORIN D
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN D / IMMUNOSUPPRESSANT / CYCLOPHILIN
Function / homology
Function and homology information


: / negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis ...: / negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / Basigin interactions / protein peptidyl-prolyl isomerization / 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 / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / negative regulation of protein phosphorylation / Calcineurin activates NFAT / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / positive regulation of protein secretion / peptidylprolyl isomerase / Assembly Of The HIV Virion / Budding and maturation of HIV virion / platelet activation / platelet aggregation / neuron differentiation / positive regulation of NF-kappaB transcription factor activity / SARS-CoV-1 activates/modulates innate immune responses / integrin binding / unfolded protein binding / Platelet degranulation / protein folding / positive regulation of protein phosphorylation / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / focal adhesion / intracellular membrane-bounded organelle / 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 D, 5,7 mutation / : / Peptidyl-prolyl cis-trans isomerase A / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / PROTEIN STRUCTURE KNOWN IN THIS CELL / Resolution: 1.8 Å
AuthorsMikol, V. / Kallen, J. / Taylor, P. / Walkinshaw, M.D.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: X-Ray Structures and Analysis of 11 Cyclosporin Derivatives Complexed with Cyclophilin A.
Authors: Kallen, J. / Mikol, V. / Taylor, P. / Walkinshaw, M.D.
History
DepositionMay 26, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: 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 1.5Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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 A
C: CYCLOSPORIN D


Theoretical massNumber of molelcules
Total (without water)19,3192
Polymers19,3192
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-8 kcal/mol
Surface area7730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.400, 60.600, 72.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 18036.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: CYCLOPHILIN / Gene (production host): CYCLOPHILIN / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P05092, UniProt: P62937*PLUS, peptidylprolyl isomerase
#2: Protein/peptide CYCLOSPORIN D / CYCLOSPORINE / CICLOSPORIN / CICLOSPORINE


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1282.759 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically
Details: (2-S-METHYL) SARCOSINE AT POSITION 7,(6,7-DIHYDRO)4-[(E)-BUTENYL]-4, N-DIMETHYL-THREONINE AT POSITION 5, CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND ...Details: (2-S-METHYL) SARCOSINE AT POSITION 7,(6,7-DIHYDRO)4-[(E)-BUTENYL]-4, N-DIMETHYL-THREONINE AT POSITION 5, CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. CYCLOSPORIN D IS A NATURAL ANALOG OF CYCLOSPORIN A, OBTAINED IN DIFFERENT NUTRIENT BROTH AND DIFFERS FROM CYCLOSPORIN IN RESIDUE 6 (ABA6VAL). THE CYCLOSPORIN D MOLECULE WAS MODIFIED AT POSITIONS 5 AND 7 TO BE (6,7-DIHYDRO)4-[(E)-BUTENYL]-4,N-DIMETHYL-THREONINE AND (2-S-METHYL)-SARCOSINE, RESPECTIVELY.
Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00036, CYCLOSPORIN D, 5,7 mutation
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN D IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 41 %
Crystal growpH: 8 / Details: PH 8.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris-HCl1reservoir
219 %(w/v)PEG80001reservoir
36 %(v/v)DMSO1reservoir
40.04 %(w/v)1reservoirNaN3
550 mMTris-HCl1drop
69.5 %PEG80001drop
73 %DMSO1drop
80.02 %1dropNaN3
90.5 mMCsA-analogue1drop
100.5 mMCypA1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS / Detector: AREA DETECTOR / Date: Jun 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 14288 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rsym value: 0.058
Reflection
*PLUS
Num. measured all: 45753 / Rmerge(I) obs: 0.058

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: PROTEIN STRUCTURE KNOWN IN THIS CELL
Starting model: PDB ENTRY 1CWF

1cwf


Resolution: 1.8→8 Å / Data cutoff high absF: 30000 / Data cutoff low absF: 0.1 / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.165 --
obs0.165 12960 92.3 %
Displacement parametersBiso mean: 18.87 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 0 149 1503
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.64
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
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2PARAM19.SOL

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