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- PDB-8c3c: 14-3-3 sigma with Pin1 binding site pS72 and bound Fusicoccin A -

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Basic information

Entry
Database: PDB / ID: 8c3c
Title14-3-3 sigma with Pin1 binding site pS72 and bound Fusicoccin A
Components
  • 14-3-3 protein sigma
  • Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 sigma / Pin1 / stabilizer / Fusicoccin A
Function / homology
Function and homology information


cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of amyloid-beta formation ...cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of amyloid-beta formation / negative regulation of SMAD protein signal transduction / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / PI5P Regulates TP53 Acetylation / cytoskeletal motor activity / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein peptidyl-prolyl isomerization / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein dephosphorylation / RHO GTPases activate PKNs / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / stem cell proliferation / Negative regulators of DDX58/IFIH1 signaling / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / synapse organization / phosphoprotein binding / regulation of protein phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein kinase activity / tau protein binding / regulation of protein stability / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / neuron differentiation / beta-catenin binding / positive regulation of GTPase activity / positive regulation of canonical Wnt signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of protein binding / midbody / positive regulation of cell growth / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / regulation of cell cycle / nuclear speck / cadherin binding / cell cycle / positive regulation of protein phosphorylation / glutamatergic synapse / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / 14-3-3 protein sigma / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. ...Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / 14-3-3 protein sigma / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
FUSICOCCIN / 14-3-3 protein sigma / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVerhoef, C.J. / Cossar, P.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: Chem Sci / Year: 2023
Title: Tracking the mechanism of covalent molecular glue stabilization using native mass spectrometry.
Authors: Verhoef, C.J.A. / Kay, D.F. / van Dijck, L. / Doveston, R.G. / Brunsveld, L. / Leney, A.C. / Cossar, P.J.
History
DepositionDec 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4594
Polymers28,7542
Non-polymers7052
Water3,855214
1
A: 14-3-3 protein sigma
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules

A: 14-3-3 protein sigma
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9198
Polymers57,5094
Non-polymers1,4104
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5660 Å2
ΔGint-50 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.847, 111.544, 62.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-612-

HOH

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26558.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / Peptidyl-prolyl cis-trans isomerase Pin1 / PPIase Pin1 / Rotamase Pin1


Mass: 2195.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13526, peptidylprolyl isomerase
#3: Chemical ChemComp-FSC / FUSICOCCIN / Fusicoccin


Mass: 680.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56O12 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: HEPES, magnesium chloride, calcium chloride, 2-mercaptoethanol, PEG400, glycerol, DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972425 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972425 Å / Relative weight: 1
ReflectionResolution: 1.6→66.51 Å / Num. obs: 73894 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 19.8 Å2 / CC1/2: 0.999 / Net I/σ(I): 30.1
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 7.1 / Num. unique obs: 1879 / CC1/2: 0.987

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Processing

Software
NameVersionClassification
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMAC5refinement
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.54 Å / SU ML: 0.1442 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1996 3840 5.2 %
Rwork0.1916 70054 -
obs0.192 73894 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 49 214 2094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242012
X-RAY DIFFRACTIONf_angle_d1.42522739
X-RAY DIFFRACTIONf_chiral_restr0.0854308
X-RAY DIFFRACTIONf_plane_restr0.0071355
X-RAY DIFFRACTIONf_dihedral_angle_d15.7635744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.19081430.23532615X-RAY DIFFRACTION100
1.62-1.640.231440.21262603X-RAY DIFFRACTION100
1.64-1.660.23311430.20622569X-RAY DIFFRACTION99.82
1.66-1.690.19911430.21772581X-RAY DIFFRACTION99.96
1.69-1.710.28121430.212579X-RAY DIFFRACTION100
1.71-1.740.24181420.2062620X-RAY DIFFRACTION100
1.74-1.770.20471400.20432613X-RAY DIFFRACTION100
1.77-1.80.22481420.20782573X-RAY DIFFRACTION99.93
1.8-1.830.20771450.19792620X-RAY DIFFRACTION100
1.83-1.870.2041390.20832568X-RAY DIFFRACTION100
1.87-1.90.20061390.20722598X-RAY DIFFRACTION100
1.9-1.950.22161400.21352601X-RAY DIFFRACTION100
1.95-1.990.22071460.21022587X-RAY DIFFRACTION100
1.99-2.040.20951420.20262590X-RAY DIFFRACTION100
2.04-2.10.19971380.18382573X-RAY DIFFRACTION100
2.1-2.160.19931450.18612628X-RAY DIFFRACTION100
2.16-2.230.20061430.18032602X-RAY DIFFRACTION100
2.23-2.310.16341400.18292588X-RAY DIFFRACTION100
2.31-2.40.20541440.18932584X-RAY DIFFRACTION100
2.4-2.510.23921400.19722604X-RAY DIFFRACTION100
2.51-2.640.19051440.18952555X-RAY DIFFRACTION100
2.64-2.810.22231440.19982610X-RAY DIFFRACTION100
2.81-3.020.20241460.19992620X-RAY DIFFRACTION100
3.02-3.330.18911400.18472595X-RAY DIFFRACTION100
3.33-3.810.20741390.18662576X-RAY DIFFRACTION100
3.81-4.790.16651440.16622595X-RAY DIFFRACTION100
4.8-34.540.18471420.19562607X-RAY DIFFRACTION99.93

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