+Open data
-Basic information
Entry | Database: PDB / ID: 6i42 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the alpha-Synuclein PreNAC/Cyclophilin A-complex | ||||||
Components |
| ||||||
Keywords | ISOMERASE / cyclophilin A / peptidyl-prolyl isomerase / alpha-Synuclein / PreNAC | ||||||
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 / negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity ...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 / negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / regulation of viral genome replication / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / leukocyte chemotaxis / response to iron(II) ion / negative regulation of stress-activated MAPK cascade / endothelial cell activation / virion binding / regulation of norepinephrine uptake / Basigin interactions / dopamine biosynthetic process / SNARE complex assembly / positive regulation of neurotransmitter secretion / regulation of locomotion / synaptic vesicle priming / positive regulation of inositol phosphate biosynthetic process / regulation of macrophage activation / dopamine uptake involved in synaptic transmission / negative regulation of microtubule polymerization / synaptic vesicle transport / cyclosporin A binding / dynein complex binding / positive regulation of receptor recycling / regulation of dopamine secretion / Minus-strand DNA synthesis / Plus-strand DNA synthesis / protein kinase inhibitor activity / Uncoating of the HIV Virion / negative regulation of thrombin-activated receptor signaling pathway / response to type II interferon / cuprous ion binding / Early Phase of HIV Life Cycle / mitochondrial ATP synthesis coupled electron transport / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / Integration of provirus / kinesin binding / APOBEC3G mediated resistance to HIV-1 infection / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / synaptic vesicle endocytosis / Calcineurin activates NFAT / regulation of presynapse assembly / alpha-tubulin binding / viral release from host cell / negative regulation of serotonin uptake / Binding and entry of HIV virion / positive regulation of viral genome replication / localization / phospholipid metabolic process / protein peptidyl-prolyl isomerization / axon terminus / supramolecular fiber organization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / inclusion body / positive regulation of protein dephosphorylation / cellular response to copper ion / Hsp70 protein binding / cellular response to epinephrine stimulus / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / excitatory postsynaptic potential / activation of protein kinase B activity / response to interleukin-1 / adult locomotory behavior / neutrophil chemotaxis / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / fatty acid metabolic process / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / long-term synaptic potentiation / positive regulation of protein secretion / regulation of transmembrane transporter activity / protein tetramerization Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 Å | ||||||
Authors | Favretto, F. / Zweckstetter, M. / Becker, S. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6i42.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6i42.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 6i42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/6i42 ftp://data.pdbj.org/pub/pdb/validation_reports/i4/6i42 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5kulS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | 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 | 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.63 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 1.93 M tri-ammonium citrate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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 |
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.21 Å2 / Biso mean: 24.349 Å2 / Biso min: 14.95 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.38→44.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.379→1.415 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|