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- PDB-5a0e: Crystal structure of cyclophilin D in complex with CsA analogue, JW47. -

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Basic information

Entry
Database: PDB / ID: 5a0e
TitleCrystal structure of cyclophilin D in complex with CsA analogue, JW47.
Components
  • JW47
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL
KeywordsISOMERASE / CYCLOPHILIN D / CYP D / PPIF / CYCLOSPORIN A / CSA / JW47 / MITOCHONDRIAL PERMEABILITY TRANSITION PORE / PTP / PEPTIDYLPROLYL CIS-TRANS ISOMERASE / CYCLOPHILIN
Function / homology
Function and homology information


: / : / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / mitochondrial depolarization / negative regulation of oxidative phosphorylation ...: / : / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / mitochondrial depolarization / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / necroptotic process / apoptotic mitochondrial changes / cellular response to calcium ion / response to ischemia / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cellular response to hydrogen peroxide / protein folding / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / 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
Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
CYLINDROCARPON LUCIDUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsWarne, J. / Pryce, G. / Hill, J. / Shi, X. / Lenneras, F. / Puentes, F. / Kip, M. / Hilditch, L. / Walker, P. / Simone, M. ...Warne, J. / Pryce, G. / Hill, J. / Shi, X. / Lenneras, F. / Puentes, F. / Kip, M. / Hilditch, L. / Walker, P. / Simone, M. / Chan, A.W.E. / Towers, G. / Coker, A.R. / Duchen, M. / Szabadkai, G. / Baker, D. / Selwood, D.L.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Selective Inhibition of the Mitochondrial Permeability Transition Pore Protects Against Neuro-Degeneration in Experimental Multiple Sclerosis.
Authors: Warne, J. / Pryce, G. / Hill, J. / Shi, X. / Lenneras, F. / Puentes, F. / Kip, M. / Hilditch, L. / Walker, P. / Simone, M.I. / Chan, A.W.E. / Towers, G.J. / Coker, A.R. / Duchen, M.R. / ...Authors: Warne, J. / Pryce, G. / Hill, J. / Shi, X. / Lenneras, F. / Puentes, F. / Kip, M. / Hilditch, L. / Walker, P. / Simone, M.I. / Chan, A.W.E. / Towers, G.J. / Coker, A.R. / Duchen, M.R. / Szabadkai, G. / Baker, D. / Selwood, D.L.
History
DepositionApr 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 F, MITOCHONDRIAL
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL
C: JW47
E: JW47


Theoretical massNumber of molelcules
Total (without water)38,2324
Polymers38,2324
Non-polymers00
Water5,477304
1
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL
C: JW47


Theoretical massNumber of molelcules
Total (without water)19,1162
Polymers19,1162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-8.9 kcal/mol
Surface area7720 Å2
MethodPISA
2
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL
E: JW47


Theoretical massNumber of molelcules
Total (without water)19,1162
Polymers19,1162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-8.5 kcal/mol
Surface area7630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.120, 69.510, 109.170
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 F, MITOCHONDRIAL / PPIASE F / 5.2.1.8 / CYCLOPHILIN D / CYP-D / CYPD / CYCLOPHILIN F / MITOCHONDRIAL CYCLOPHILIN / CYP- ...PPIASE F / 5.2.1.8 / CYCLOPHILIN D / CYP-D / CYPD / CYCLOPHILIN F / MITOCHONDRIAL CYCLOPHILIN / CYP-M / ROTAMASE F


Mass: 17739.205 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P30405, peptidylprolyl isomerase
#2: Protein/peptide JW47


Mass: 1376.829 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: CYCLOSPORINE A WITH 1-(PENT-4-ENYL) QUINOLINIUM LINKED TO THE BMT RESIDUE.
Source: (synth.) CYLINDROCARPON LUCIDUM (fungus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE (BMT): 1-PENT-4-ENYL QUINOLINIUM LINKED TO CH OF ...4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE (BMT): 1-PENT-4-ENYL QUINOLINIUM LINKED TO CH OF BMT 1-(PENT-4-ENYL)QUINOLINIUM (DRG): LINKED TO CH OF BMT
Sequence detailsK133I MUTATION

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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: 2.04 Å3/Da / Density % sol: 39.6 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 2.9
Details: HANGING DROP 50:50. PRECIPITANT: 23% POLYETHYLENE GLYCOL (PEG3350), 50 MM SODIUM-CITRATE BUFFER AT PH 2.9 PROTEIN: 30 MG/ML IN 50MM POTASSIUM/SODIUM PHOSPHATE PH 7.3, 100MM NACL, 2MM EDTA, 0.02% SODIUM AZIDE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9174
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 1.12→35.99 Å / Num. obs: 101898 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.4
Reflection shellResolution: 1.12→1.15 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.8 / % possible all: 45.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z6W

2z6w


Resolution: 1.25→35.99 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.994 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.13122 3964 5 %RANDOM
Rwork0.09806 ---
obs0.09971 75156 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.25→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 0 304 2984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192813
X-RAY DIFFRACTIONr_bond_other_d0.0020.022712
X-RAY DIFFRACTIONr_angle_refined_deg2.1371.9953815
X-RAY DIFFRACTIONr_angle_other_deg3.10136263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7655348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.95324.299107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97615450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7511510
X-RAY DIFFRACTIONr_chiral_restr0.30.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213234
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02626
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6781.1851430
X-RAY DIFFRACTIONr_mcbond_other2.6771.1841429
X-RAY DIFFRACTIONr_mcangle_it3.31.7861788
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2041.51383
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.19335525
X-RAY DIFFRACTIONr_sphericity_free30.806595
X-RAY DIFFRACTIONr_sphericity_bonded11.73655667
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.167 297 -
Rwork0.113 5143 -
obs--91.69 %

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