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- PDB-6i42: Structure of the alpha-Synuclein PreNAC/Cyclophilin A-complex -

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Basic information

Entry
Database: PDB / ID: 6i42
TitleStructure of the alpha-Synuclein PreNAC/Cyclophilin A-complex
Components
  • Alpha-synuclein
  • Peptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / cyclophilin A / peptidyl-prolyl isomerase / alpha-Synuclein / PreNAC
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of mitochondrial electron transport, NADH to ubiquinone ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of stress-activated MAPK cascade / regulation of synaptic vesicle recycling / endothelial cell activation / negative regulation of chaperone-mediated autophagy / mitochondrial membrane organization / regulation of reactive oxygen species biosynthetic process / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / regulation of glutamate secretion / Basigin interactions / protein peptidyl-prolyl isomerization / dopamine biosynthetic process / response to iron(II) ion / cyclosporin A binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / regulation of locomotion / negative regulation of dopamine metabolic process / positive regulation of inositol phosphate biosynthetic process / regulation of macrophage activation / Minus-strand DNA synthesis / Plus-strand DNA synthesis / negative regulation of microtubule polymerization / regulation of norepinephrine uptake / Uncoating of the HIV Virion / synaptic vesicle transport / transporter regulator activity / synaptic vesicle priming / dopamine uptake involved in synaptic transmission / Early Phase of HIV Life Cycle / protein kinase inhibitor activity / mitochondrial ATP synthesis coupled electron transport / Integration of provirus / regulation of dopamine secretion / negative regulation of protein phosphorylation / dynein complex binding / negative regulation of thrombin-activated receptor signaling pathway / APOBEC3G mediated resistance to HIV-1 infection / positive regulation of receptor recycling / cuprous ion binding / nuclear outer membrane / viral release from host cell / response to magnesium ion / positive regulation of endocytosis / positive regulation of exocytosis / synaptic vesicle exocytosis / Calcineurin activates NFAT / kinesin binding / synaptic vesicle endocytosis / enzyme inhibitor activity / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / activation of protein kinase B activity / response to type II interferon / Binding and entry of HIV virion / regulation of presynapse assembly / alpha-tubulin binding / beta-tubulin binding / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / phospholipase binding / behavioral response to cocaine / supramolecular fiber organization / phospholipid metabolic process / cellular response to fibroblast growth factor stimulus / inclusion body / axon terminus / Hsp70 protein binding / neutrophil chemotaxis / cellular response to epinephrine stimulus / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / response to interleukin-1 / regulation of microtubule cytoskeleton organization / cellular response to copper ion / positive regulation of release of sequestered calcium ion into cytosol / adult locomotory behavior / SNARE binding / positive regulation of protein secretion / excitatory postsynaptic potential
Similarity search - Function
Cyclophilin-like / Cyclophilin / Synuclein / Alpha-synuclein / Synuclein / 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-like / Cyclophilin / Synuclein / Alpha-synuclein / Synuclein / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Alpha-synuclein / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 Å
AuthorsFavretto, F. / Zweckstetter, M. / Becker, S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: The Molecular Basis of the Interaction of Cyclophilin A with alpha-Synuclein.
Authors: Favretto, F. / Baker, J.D. / Strohaker, T. / Andreas, L.B. / Blair, L.J. / Becker, S. / Zweckstetter, M.
History
DepositionNov 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: 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
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase A
B: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)19,2472
Polymers19,2472
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-5 kcal/mol
Surface area8480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.034, 61.034, 129.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 17905.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Plasmid: pET28a / Details (production host): engineered TEV cleavage site / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62937, peptidylprolyl isomerase
#2: Protein/peptide Alpha-synuclein / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP


Mass: 1341.574 Da / Num. of mol.: 1 / Fragment: UNP residues 48-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Production host: synthetic construct (others) / References: UniProt: P37840
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 1.93 M tri-ammonium citrate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→44.4 Å / Num. obs: 51144 / % possible obs: 99.7 % / Redundancy: 24.01 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 27.39
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
1.38-1.412.560.8081153192.6
1.4-1.4317.720.7882998198.9
1.43-1.4623.10.7252779199.6
1.46-1.4924.740.6582562199.8
1.49-1.5324.840.57631471100
1.53-1.5724.730.49428001100
1.57-1.6223.690.4131591100
1.62-1.6725.280.31928041100
1.67-1.7326.340.26229071100
1.73-1.826.020.19929631100
1.8-1.8825.260.14628551100
1.88-1.9724.320.11526971100
1.97-2.0826.520.08926841100
2.08-2.2225.940.07427081100
2.22-2.424.490.06526241100
2.4-2.6524.580.05825671100
2.65-3.0524.890.05225901100
3.05-3.8922.390.04625771100
3.89-44.3622.750.0362570199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XPREP2008/2data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5kul

5kul


Resolution: 1.38→44.4 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.833 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.047
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1778 2548 5 %RANDOM
Rwork0.1631 ---
obs0.1639 48509 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.21 Å2 / Biso mean: 24.349 Å2 / Biso min: 14.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 1.38→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 10 255 1612
Biso mean--31.84 37.79 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131480
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181372
X-RAY DIFFRACTIONr_angle_refined_deg2.1821.6521996
X-RAY DIFFRACTIONr_angle_other_deg1.6171.5933205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.275195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76522.91772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90715264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.108157
X-RAY DIFFRACTIONr_chiral_restr0.1240.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021730
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02323
LS refinement shellResolution: 1.379→1.415 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 176 -
Rwork0.292 3440 -
all-3616 -
obs--96.89 %

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