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- PDB-7az2: 14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1014 -

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Basic information

Entry
Database: PDB / ID: 7az2
Title14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1014
Components
  • 14-3-3 protein sigma
  • Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsPEPTIDE BINDING PROTEIN / 1433 / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
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 SMAD protein signal transduction ...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 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 / 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 / stem cell proliferation / peptidyl-prolyl cis-trans isomerase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Negative regulators of DDX58/IFIH1 signaling / TP53 Regulates Metabolic Genes / synapse organization / phosphoprotein binding / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein phosphorylation / negative regulation of protein kinase activity / regulation of protein stability / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / tau protein binding / negative regulation of ERK1 and ERK2 cascade / negative regulation of protein catabolic process / neuron differentiation / ISG15 antiviral mechanism / 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 / positive regulation of protein phosphorylation / cell cycle / 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
Chem-SFW / 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 / molecular replacement / Resolution: 1.081 Å
AuthorsWolter, M. / Dijck, L.v. / Ottmann, C.
Funding support2items
OrganizationGrant numberCountry
European Commission675179
European Commission754462
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Reversible Covalent Imine-Tethering for Selective Stabilization of 14-3-3 Hub Protein Interactions.
Authors: Cossar, P.J. / Wolter, M. / van Dijck, L. / Valenti, D. / Levy, L.M. / Ottmann, C. / Brunsveld, L.
History
DepositionNov 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 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

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)30,7836
Polymers30,3652
Non-polymers4184
Water6,341352
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)61,56612
Polymers60,7304
Non-polymers8368
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4740 Å2
ΔGint-62 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.142, 112.024, 62.456
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-303-

CA

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

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


Mass: 28169.469 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

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Non-polymers , 4 types, 356 molecules

#3: Chemical ChemComp-SFW / 1-[4-methyl-2-(trifluoromethyl)phenyl]-2-phenyl-imidazole


Mass: 302.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13F3N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.095 M HEPES Na pH 7.1, 27% PEG400, 0.19M Calcium chloride, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.08→66.242 Å / Num. obs: 119445 / % possible obs: 97.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 13.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Rrim(I) all: 0.039 / Rsym value: 0.027 / Net I/σ(I): 14.1
Reflection shellResolution: 1.08→1.1 Å / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4601 / CC1/2: 0.425 / Rpim(I) all: 0.684 / Rrim(I) all: 0.967 / % possible all: 76.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12refinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AOG

7aog


Resolution: 1.081→66.242 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1974 5967 5 %
Rwork0.1846 219452 -
obs0.1853 119245 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.18 Å2 / Biso mean: 21.3611 Å2 / Biso min: 10.57 Å2
Refinement stepCycle: final / Resolution: 1.081→66.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 25 352 2233
Biso mean--40.48 33.92 -
Num. residues----237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052056
X-RAY DIFFRACTIONf_angle_d0.7422799
X-RAY DIFFRACTIONf_chiral_restr0.059301
X-RAY DIFFRACTIONf_plane_restr0.005372
X-RAY DIFFRACTIONf_dihedral_angle_d10.0311178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.081-1.09280.35343330.3522531071
1.0928-1.10560.35553150.3304596179
1.1056-1.11910.31253330.3125640285
1.1191-1.13330.28623760.2862687191
1.1333-1.14820.27254550.2696705495
1.1482-1.16390.2533620.2525735997
1.1639-1.18060.25864010.2404741498
1.1806-1.19820.2463940.2362750199
1.1982-1.21690.24143880.22877452100
1.2169-1.23690.23974210.22867423100
1.2369-1.25820.25144080.22257560100
1.2582-1.28110.274220.22157542100
1.2811-1.30570.24463910.21337533100
1.3057-1.33240.21334100.21337570100
1.3324-1.36130.25414180.20887502100
1.3613-1.3930.20274120.20277584100
1.393-1.42790.21623860.20297478100
1.4279-1.46650.22843750.19497559100
1.4665-1.50960.19713660.18487659100
1.5096-1.55840.21853970.18687505100
1.5584-1.61410.19413660.18427602100
1.6141-1.67870.18113980.17657528100
1.6787-1.75510.20254520.18477482100
1.7551-1.84760.20523570.18297563100
1.8476-1.96340.19523910.17777572100
1.9634-2.1150.1773910.17087586100
2.115-2.32780.18123810.15827578100
2.3278-2.66470.16743860.16747584100
2.6647-3.35720.17833500.17167568100
3.3572-66.2420.1813170.1744715094

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