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- PDB-2esl: Human Cyclophilin C in Complex with Cyclosporin A -

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Basic information

Entry
Database: PDB / ID: 2esl
TitleHuman Cyclophilin C in Complex with Cyclosporin A
Components
  • CYCLOSPORIN ACiclosporin
  • Peptidyl-prolyl cis-trans isomerase C
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPRESSANT / CYCLOPHILIN / SGC / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


cyclosporin A binding / protein peptidyl-prolyl isomerization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / extracellular exosome / 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 speciesHomo sapiens (human)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWalker, J.R. / Davis, T. / Newman, E.M. / Finerty Jr., P.J. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. ...Walker, J.R. / Davis, T. / Newman, E.M. / Finerty Jr., P.J. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: PLoS Biol. / Year: 2010
Title: Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases.
Authors: Davis, T.L. / Walker, J.R. / Campagna-Slater, V. / Finerty, P.J. / Paramanathan, R. / Bernstein, G. / MacKenzie, F. / Tempel, W. / Ouyang, H. / Lee, W.H. / Eisenmesser, E.Z. / Dhe-Paganon, S.
History
DepositionOct 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: 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 1.5Jun 21, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_entry_details.sequence_details
Revision 1.6Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: Peptidyl-prolyl cis-trans isomerase C
C: Peptidyl-prolyl cis-trans isomerase C
D: Peptidyl-prolyl cis-trans isomerase C
E: Peptidyl-prolyl cis-trans isomerase C
F: Peptidyl-prolyl cis-trans isomerase C
I: CYCLOSPORIN A
J: CYCLOSPORIN A
K: CYCLOSPORIN A
L: CYCLOSPORIN A
M: CYCLOSPORIN A
N: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,40523
Polymers130,57812
Non-polymers82711
Water14,376798
1
A: Peptidyl-prolyl cis-trans isomerase C
I: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9655
Polymers21,7632
Non-polymers2023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-20 kcal/mol
Surface area8700 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase C
J: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8593
Polymers21,7632
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-20 kcal/mol
Surface area8680 Å2
MethodPISA
3
C: Peptidyl-prolyl cis-trans isomerase C
K: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8593
Polymers21,7632
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-20 kcal/mol
Surface area8590 Å2
MethodPISA
4
D: Peptidyl-prolyl cis-trans isomerase C
L: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9655
Polymers21,7632
Non-polymers2023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-20 kcal/mol
Surface area8820 Å2
MethodPISA
5
E: Peptidyl-prolyl cis-trans isomerase C
M: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8593
Polymers21,7632
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-20 kcal/mol
Surface area8620 Å2
MethodPISA
6
F: Peptidyl-prolyl cis-trans isomerase C
N: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8994
Polymers21,7632
Non-polymers1362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-28 kcal/mol
Surface area8550 Å2
MethodPISA
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17950 Å2
ΔGint-320 kcal/mol
Surface area41220 Å2
MethodPISA
8
A: Peptidyl-prolyl cis-trans isomerase C
B: Peptidyl-prolyl cis-trans isomerase C
C: Peptidyl-prolyl cis-trans isomerase C
I: CYCLOSPORIN A
J: CYCLOSPORIN A
K: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,68311
Polymers65,2896
Non-polymers3945
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-136 kcal/mol
Surface area22490 Å2
MethodPISA
9
D: Peptidyl-prolyl cis-trans isomerase C
E: Peptidyl-prolyl cis-trans isomerase C
F: Peptidyl-prolyl cis-trans isomerase C
L: CYCLOSPORIN A
M: CYCLOSPORIN A
N: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,72312
Polymers65,2896
Non-polymers4346
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-143 kcal/mol
Surface area22510 Å2
MethodPISA
10
B: Peptidyl-prolyl cis-trans isomerase C
D: Peptidyl-prolyl cis-trans isomerase C
J: CYCLOSPORIN A
L: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8248
Polymers43,5264
Non-polymers2984
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-55 kcal/mol
Surface area16470 Å2
MethodPISA
11
A: Peptidyl-prolyl cis-trans isomerase C
E: Peptidyl-prolyl cis-trans isomerase C
I: CYCLOSPORIN A
M: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8248
Polymers43,5264
Non-polymers2984
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-54 kcal/mol
Surface area16320 Å2
MethodPISA
12
C: Peptidyl-prolyl cis-trans isomerase C
F: Peptidyl-prolyl cis-trans isomerase C
K: CYCLOSPORIN A
N: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7587
Polymers43,5264
Non-polymers2323
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-61 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.203, 123.802, 135.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 12 molecules ABCDEFIJKLMN

#1: Protein
Peptidyl-prolyl cis-trans isomerase C / PPIase C / Cyclophilin C / Rotamase C


Mass: 20542.375 Da / Num. of mol.: 6 / Fragment: RESIDUES 24-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIC, CYPC / Plasmid: PET28-LIC / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45877, peptidylprolyl isomerase
#2: Protein/peptide
CYCLOSPORIN A / Ciclosporin / Ciclosporin


Type: Cyclic peptide / Class: ImmunosuppressantImmunosuppressive drug / Mass: 1220.625 Da / Num. of mol.: 6 / 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

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Non-polymers , 4 types, 809 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 798 / Source method: isolated from a natural source / Formula: H2O

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Details

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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growpH: 6.5
Details: 25% PEG550 MME, 10MM ZINC ACETATE, 100MM MES, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97949
DetectorType: SBC-3 / Detector: CCD / Date: Jun 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→36.4 Å / Num. obs: 95283 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 25.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 3.68 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→36.4 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.007 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4733 5 %RANDOM
Rwork0.178 ---
obs0.18 90042 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2---1.46 Å20 Å2
3---2.52 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8826 0 35 798 9659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229048
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.96812258
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26551104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36324.138348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.992151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0541530
X-RAY DIFFRACTIONr_chiral_restr0.0960.21386
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026774
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.24316
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.26233
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2770
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3380.214
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1640.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.72635802
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.59749180
X-RAY DIFFRACTIONr_scbond_it3.34953654
X-RAY DIFFRACTIONr_scangle_it4.9273078
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 332 -
Rwork0.227 6515 -
obs--97.61 %

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