[English] 日本語
Yorodumi
- PDB-6i42: Structure of the alpha-Synuclein PreNAC/Cyclophilin A-complex -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / 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 / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / neutral lipid metabolic process / leukocyte chemotaxis / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of synaptic vesicle recycling / negative regulation of stress-activated MAPK cascade / 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 / endothelial cell activation / response to iron(II) ion / SNARE complex assembly / Basigin interactions / protein peptidyl-prolyl isomerization / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of norepinephrine uptake / transporter regulator activity / regulation of locomotion / mitochondrial ATP synthesis coupled electron transport / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / cyclosporin A binding / negative regulation of microtubule polymerization / synaptic vesicle transport / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / positive regulation of receptor recycling / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / dynein complex binding / Early Phase of HIV Life Cycle / regulation of dopamine secretion / negative regulation of thrombin-activated receptor signaling pathway / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / cuprous ion binding / positive regulation of endocytosis / positive regulation of exocytosis / response to magnesium ion / synaptic vesicle exocytosis / enzyme inhibitor activity / viral release from host cell / kinesin binding / negative regulation of protein phosphorylation / Calcineurin activates NFAT / synaptic vesicle endocytosis / regulation of presynapse assembly / response to type II interferon / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / alpha-tubulin binding / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / supramolecular fiber organization / inclusion body / phospholipid metabolic process / cellular response to copper ion / axon terminus / cellular response to epinephrine stimulus / neutrophil chemotaxis / Hsp70 protein binding / response to interleukin-1 / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / regulation of microtubule cytoskeleton organization / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / adult locomotory behavior / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / excitatory postsynaptic potential / fatty acid metabolic process / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / positive regulation of protein secretion / peptidylprolyl isomerase / phosphoprotein binding / protein tetramerization
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein / Cyclophilin-like / Cyclophilin / 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 ...Synuclein / Alpha-synuclein / Synuclein / Cyclophilin-like / Cyclophilin / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more