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- PDB-8ejx: Crystal structure of human cyclophilin D (CypD) with in complex w... -

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Basic information

Entry
Database: PDB / ID: 8ejx
TitleCrystal structure of human cyclophilin D (CypD) with in complex with the covalently bound Ebselen inhibitor
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE
Function / homology
Function and homology information


regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / 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 / negative regulation of ATP-dependent activity / cellular response to arsenic-containing substance / mitochondrial depolarization / negative regulation of oxidative phosphorylation ...regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / 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 / negative regulation of ATP-dependent activity / cellular response to arsenic-containing substance / mitochondrial depolarization / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / necroptotic process / apoptotic mitochondrial changes / protein peptidyl-prolyl isomerization / negative regulation of intrinsic apoptotic signaling pathway / cellular response to calcium ion / peptidylprolyl isomerase / response to ischemia / peptidyl-prolyl cis-trans isomerase activity / peptide binding / 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
N-phenyl-2-selanylbenzamide / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsLovell, S. / Battaile, K.P. / Yan, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R37AG037319 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG069426 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG61324 United States
CitationJournal: Brain / Year: 2024
Title: New cyclophilin D inhibitor rescues mitochondrial and cognitive function in Alzheimer's disease.
Authors: Samanta, S. / Akhter, F. / Roy, A. / Chen, D. / Turner, B. / Wang, Y. / Clemente, N. / Wang, C. / Swerdlow, R.H. / Battaile, K.P. / Lovell, S. / Yan, S.F. / Yan, S.S.
History
DepositionSep 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0312
Polymers17,7551
Non-polymers2761
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.014, 57.014, 87.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

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Components

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


Mass: 17755.205 Da / Num. of mol.: 1 / Mutation: K133I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Plasmid: pET-21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30405, peptidylprolyl isomerase
#2: Chemical ChemComp-9JT / N-phenyl-2-selanylbenzamide / ~{N}-phenyl-2-selanyl-benzamide / Ebselen, bound form


Mass: 276.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11NOSe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% (w/v) PEG 4000, 100 mM Hepes, 200 NaCl

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2016
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→47.78 Å / Num. obs: 18096 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 25.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19 / Num. measured all: 227474 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.65-1.6812.91.745114138880.6581.6100
9.04-47.788.80.03313381520.99752.899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.25data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O8H

4o8h


Resolution: 1.65→36.62 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 19.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1984 897 4.97 %
Rwork0.1641 17139 -
obs0.1657 18036 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.54 Å2 / Biso mean: 28.453 Å2 / Biso min: 14.76 Å2
Refinement stepCycle: final / Resolution: 1.65→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 16 115 1339
Biso mean--43.24 33.3 -
Num. residues----164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.65-1.750.3021490.288727922941
1.75-1.890.25251510.203227852936
1.89-2.080.20951570.159427912948
2.08-2.380.2091520.152728543006
2.38-30.17871370.171928743011
3-36.620.18351510.150830433194
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.82770.853-0.55532.833-0.04821.5891-0.082-0.0406-0.1006-0.22460.00910.18650.2331-0.2173-0.02050.2209-0.0168-0.00050.13720.00670.207366.602938.215692.5114
23.285-0.9311.03162.0284-1.44533.6048-0.0733-0.22040.18020.11570.04140.2228-0.1067-0.32240.05050.1780.00950.00280.161-0.01760.213463.878748.410196.911
32.0361-2.4931-1.72315.24820.2775.01770.01020.56470.2603-0.81420.0648-0.50670.30780.3496-0.03320.3535-0.00520.03250.2497-0.00890.238473.459944.73179.2027
40.70780.3265-0.53341.77751.21493.875-0.0740.12460.2718-0.21820.18260.2391-0.3957-0.0769-0.06040.2885-0.0036-0.02210.21090.01660.287666.468955.483988.9698
51.84230.36270.18632.34340.40561.47090.01130.02910.0065-0.25330.0006-0.27080.00620.1843-0.0190.2043-0.00310.01540.1720.00970.200777.984349.014192.6297
65.2345-1.003-0.34449.84092.77525.3511-0.11570.8134-0.1018-0.59640.2379-0.90170.53630.7249-0.09020.37010.01420.05660.3896-0.02080.325784.999645.821288.6778
71.62760.57690.52462.0518-0.36024.1689-0.01890.1719-0.3431-0.5445-0.09-0.24080.5335-0.23650.14490.3420.00170.03680.2141-0.02880.235271.636135.993285.7889
87.16871.4983-2.14292.2003-0.56152.9378-0.20190.67640.1661-0.61730.1835-0.13140.38410.0410.1120.6127-0.0184-0.01150.51940.10760.237169.203544.604772.8636
92.5281-0.02140.94123.5252-3.6067.8791-0.0170.03680.0121-0.24320.22860.58120.2595-0.5945-0.17030.2347-0.0243-0.030.2036-0.02060.289160.893840.220891.4522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 29 )A2 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 51 )A30 - 51
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 61 )A52 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 82 )A63 - 82
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 115 )A83 - 115
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 127 )A116 - 127
7X-RAY DIFFRACTION7chain 'A' and (resid 128 through 145 )A128 - 145
8X-RAY DIFFRACTION8chain 'A' and (resid 146 through 155 )A146 - 155
9X-RAY DIFFRACTION9chain 'A' and (resid 156 through 165 )A156 - 165

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