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- PDB-7qbw: Human Cyclophilin A double mutant C52AK125C -

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Basic information

Entry
Database: PDB / ID: 7qbw
TitleHuman Cyclophilin A double mutant C52AK125C
ComponentsPeptidyl-prolyl cis-trans isomerase A
KeywordsCYTOSOLIC PROTEIN / Peptidylprolyl isomerase / cyclophilin
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation ...negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / Basigin interactions / 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 / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / viral release from host cell / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / focal adhesion / Neutrophil degranulation / apoptotic process / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsFischer, L. / Buratto, J. / Langlois d'Estaintot, B.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE07-0034European Union
European Union (EU)H2020-MSCA-IF-2016-751019-PROFOLIGEuropean Union
CitationJournal: To Be Published
Title: Human Cyclophilin A double mutant C52AK125C
Authors: Fischer, L. / Buratto, J. / Langlois d'Estaintot, B.
History
DepositionNov 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,1633
Polymers17,9781
Non-polymers1842
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-1 kcal/mol
Surface area7450 Å2
Unit cell
Length a, b, c (Å)41.300, 54.240, 87.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


Mass: 17978.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysY / References: UniProt: P62937, peptidylprolyl isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES 60mM, NaCl 50mM, TCEP 5mM, 10% PEG 3350, NaN3 1.5mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980097 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980097 Å / Relative weight: 1
ReflectionResolution: 1.59→43.65 Å / Num. obs: 26921 / % possible obs: 98.4 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.59-1.639.31.37915270.6550.4451.45477.8
7.09-43.6510.90.0363750.9990.0110.03799.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.01 Å43.65 Å
Translation5.01 Å43.65 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PHENIXv1.17.1-3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CWA

1cwa


Resolution: 1.59→43.65 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1912 1342 5 %
Rwork0.17 25482 -
obs0.1711 26824 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.8 Å2 / Biso mean: 34.9493 Å2 / Biso min: 21.92 Å2
Refinement stepCycle: final / Resolution: 1.59→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 28 135 1412
Biso mean--72.83 46.58 -
Num. residues----164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.59-1.650.33471180.30472235235388
1.65-1.710.28271330.241125262659100
1.71-1.790.20721330.218125372670100
1.79-1.880.21571340.181325452679100
1.88-20.1961340.165825382672100
2-2.160.1981350.166825662701100
2.16-2.370.2271350.166325702705100
2.37-2.720.22231370.180625932730100
2.72-3.420.1941380.17126292767100
3.42-43.650.15371450.152827432888100
Refinement TLS params.Method: refined / Origin x: -3.9691 Å / Origin y: 9.6311 Å / Origin z: -13.7036 Å
111213212223313233
T0.2617 Å2-0.0022 Å2-0.0064 Å2-0.2235 Å20.005 Å2--0.2486 Å2
L1.524 °20.2913 °2-0.7067 °2-1.605 °20.1679 °2--2.7617 °2
S0.0517 Å °-0.0157 Å °-0.0235 Å °-0.0034 Å °0.0098 Å °0.0423 Å °0.1022 Å °-0.0287 Å °-0.062 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 165
2X-RAY DIFFRACTION1allW1 - 145
3X-RAY DIFFRACTION1allB1 - 2

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