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- PDB-8c2g: 14-3-3 sigma with Pin1 binding site pS72 and covalently bound CV1040 -

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Basic information

Entry
Database: PDB / ID: 8c2g
Title14-3-3 sigma with Pin1 binding site pS72 and covalently bound CV1040
Components
  • 14-3-3 protein sigma
  • Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 sigma / Pin1 / covalent / stabilizer
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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division ...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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / 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 / negative regulation of amyloid-beta formation / regulation of cell-cell adhesion / cytoskeletal motor activity / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / postsynaptic cytosol / 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 / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / negative regulation of protein binding / positive regulation of GTPase activity / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / peptidyl-prolyl cis-trans isomerase activity / regulation of cytokinesis / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / peptidylprolyl isomerase / phosphoprotein binding / Negative regulators of DDX58/IFIH1 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / synapse organization / negative regulation of ERK1 and ERK2 cascade / regulation of protein stability / negative regulation of protein catabolic process / beta-catenin binding / tau protein binding / ISG15 antiviral mechanism / intrinsic apoptotic signaling pathway in response to DNA damage / neuron differentiation / positive regulation of canonical Wnt signaling pathway / intracellular protein localization / regulation of protein localization / positive regulation of protein phosphorylation / regulation of gene expression / midbody / positive regulation of cell growth / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / regulation of cell cycle / protein stabilization / nuclear speck / ciliary basal body / cadherin binding / protein kinase binding / glutamatergic synapse / 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 ...: / 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
2-iodanyl-4-(2-phenylimidazol-1-yl)benzaldehyde / 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 22, 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
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
P: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1775
Polymers28,7542
Non-polymers4233
Water4,234235
1
A: 14-3-3 protein sigma
P: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)58,35410
Polymers57,5094
Non-polymers8466
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4020 Å2
ΔGint-34 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.155, 111.817, 62.682
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Components on special symmetry positions
IDModelComponents
11A-302-

MG

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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-T85 / 2-iodanyl-4-(2-phenylimidazol-1-yl)benzaldehyde


Mass: 374.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11IN2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.19 %
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: 0.9724 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: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.6→62.68 Å / Num. obs: 38472 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 17.43 Å2 / CC1/2: 0.999 / Net I/σ(I): 41.5
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 11.8 / Num. unique obs: 1873 / CC1/2: 0.991

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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→41.08 Å / SU ML: 0.1436 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.8072
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1862 3822 5.19 %RANDOM
Rwork0.179 69822 --
obs0.1794 38472 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.39 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 21 235 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01311938
X-RAY DIFFRACTIONf_angle_d1.55232631
X-RAY DIFFRACTIONf_chiral_restr0.0872289
X-RAY DIFFRACTIONf_plane_restr0.0131343
X-RAY DIFFRACTIONf_dihedral_angle_d15.297740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.22871440.23322609X-RAY DIFFRACTION100
1.62-1.640.23061460.21822631X-RAY DIFFRACTION100
1.64-1.660.18291400.19932532X-RAY DIFFRACTION99.96
1.66-1.690.20031440.19552578X-RAY DIFFRACTION99.96
1.69-1.710.21191440.18952576X-RAY DIFFRACTION100
1.71-1.740.20061350.1842586X-RAY DIFFRACTION100
1.74-1.770.16411430.18522594X-RAY DIFFRACTION100
1.77-1.80.13871410.1822587X-RAY DIFFRACTION99.96
1.8-1.830.15391420.17482594X-RAY DIFFRACTION100
1.83-1.870.19561460.1782578X-RAY DIFFRACTION100
1.87-1.90.20321410.17962588X-RAY DIFFRACTION99.96
1.9-1.950.20011440.1912582X-RAY DIFFRACTION99.96
1.95-1.990.20591410.19732590X-RAY DIFFRACTION100
1.99-2.040.18661400.18492577X-RAY DIFFRACTION100
2.04-2.10.17641400.16352590X-RAY DIFFRACTION100
2.1-2.160.16431470.17082567X-RAY DIFFRACTION100
2.16-2.230.16751370.16992619X-RAY DIFFRACTION100
2.23-2.310.19021390.16182576X-RAY DIFFRACTION100
2.31-2.40.17631390.16822579X-RAY DIFFRACTION100
2.4-2.510.20331390.18042594X-RAY DIFFRACTION100
2.51-2.640.18491380.17862565X-RAY DIFFRACTION100
2.64-2.810.20021420.18962609X-RAY DIFFRACTION100
2.81-3.020.19621450.18912586X-RAY DIFFRACTION100
3.02-3.330.17911400.17972596X-RAY DIFFRACTION100
3.33-3.810.18931380.17112557X-RAY DIFFRACTION100
3.81-4.80.1681390.1582593X-RAY DIFFRACTION99.96
4.8-41.080.19651480.19422589X-RAY DIFFRACTION99.78

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