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- PDB-9rlm: HUMAN CYCLOPHILIN D IN COMPLEX WITH INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 9rlm
TitleHUMAN CYCLOPHILIN D IN COMPLEX WITH INHIBITOR
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE / CYCLOPHILIN / BETA BARREL / PROLYL CIS/TRANS ISOMERASE / MITOC
Function / homology
Function and homology information


regulation of proton-transporting ATPase activity, rotational mechanism / : / 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 / mitochondrial depolarization / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation ...regulation of proton-transporting ATPase activity, rotational mechanism / : / 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 / mitochondrial depolarization / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / apoptotic mitochondrial changes / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / necroptotic process / peptide binding / cellular response to calcium ion / peptidyl-prolyl cis-trans isomerase activity / response to ischemia / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / cellular response to hydrogen peroxide / protein folding / mitochondrial inner membrane / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsGraedler, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HUMAN CYCLOPHILIN D IN COMPLEX WITH INHIBITOR
Authors: Graedler, U.
History
DepositionJun 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4665
Polymers17,6521
Non-polymers8144
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-3 kcal/mol
Surface area7330 Å2
Unit cell
Length a, b, c (Å)57.039, 57.039, 114.404
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidyl-prolyl cis-trans isomerase F, mitochondrial / PPIase F / Cyclophilin D / CypD / Cyclophilin F / Mitochondrial cyclophilin / CyP-M / Rotamase F


Mass: 17652.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30405, peptidylprolyl isomerase

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Non-polymers , 5 types, 220 molecules

#2: Chemical ChemComp-A1JG4 / ~{N}'-cyclopentyl-~{N}-[2-[(1~{R},9~{R},10~{S})-10-oxidanyl-12-oxa-8-azatricyclo[7.3.1.0^{2,7}]trideca-2(7),3,5-trien-4-yl]ethyl]ethanediamide


Mass: 373.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.33 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 50 mM potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→51.05 Å / Num. obs: 52891 / % possible obs: 99.7 % / Redundancy: 12.5 % / Rrim(I) all: 0.049 / Rsym value: 0.047 / Net I/σ(I): 22.99
Reflection shellResolution: 1.25→1.5 Å / Redundancy: 10.8 % / Num. unique obs: 21829 / Rrim(I) all: 0.579 / Rsym value: 0.551 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.25→18.08 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.042 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.046 / SU Rfree Blow DPI: 0.047 / SU Rfree Cruickshank DPI: 0.044
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 5339 -RANDOM
Rwork0.186 ---
obs0.188 52867 99.7 %-
Displacement parametersBiso mean: 24.11 Å2
Baniso -1Baniso -2Baniso -3
1-3.7092 Å20 Å20 Å2
2--3.7092 Å20 Å2
3----7.4183 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.25→18.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 55 217 1512
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0131331HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.261789HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d465SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes229HARMONIC5
X-RAY DIFFRACTIONt_it1331HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion165SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1384SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion5.1
X-RAY DIFFRACTIONt_other_torsion17.78
LS refinement shellResolution: 1.25→1.26 Å
RfactorNum. reflection% reflection
Rfree0.3766 105 -
Rwork0.3571 --
obs0.3591 1058 90 %
Refinement TLS params.Origin x: -10.4425 Å / Origin y: -8.6738 Å / Origin z: -22.7748 Å
111213212223313233
T0.0149 Å2-0.0012 Å20.0344 Å2--0.0277 Å2-0.0064 Å2--0.0253 Å2
L0.9779 °20.126 °2-0.4516 °2-0.2568 °2-0.152 °2--0.19 °2
S-0.0881 Å °0.0911 Å °0.018 Å °0.0911 Å °-0.021 Å °-0.0376 Å °0.018 Å °-0.0376 Å °0.1091 Å °
Refinement TLS groupSelection details: { A|* }

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