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- PDB-7axn: 14-3-3 sigma in complex with Pin1 binding site pS72 and covalentl... -

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Basic information

Entry
Database: PDB / ID: 7axn
Title14-3-3 sigma in complex with Pin1 binding site pS72 and covalently bound TCF521-026
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 / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / regulation of epidermal cell 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 / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / regulation of epidermal cell division / protein kinase C inhibitor activity / negative regulation of SMAD protein signal transduction / 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 / protein peptidyl-prolyl isomerization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / RHO GTPases activate PKNs / : / protein kinase A signaling / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of GTPase activity / positive regulation of protein export from nucleus / ciliary basal body / regulation of cytokinesis / stem cell proliferation / negative regulation of protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / peptidylprolyl isomerase / TP53 Regulates Metabolic Genes / Negative regulators of DDX58/IFIH1 signaling / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein kinase activity / synapse organization / regulation of protein phosphorylation / regulation of protein stability / tau protein binding / negative regulation of protein catabolic process / neuron differentiation / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / regulation of protein localization / midbody / regulation of gene expression / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / regulation of cell cycle / protein stabilization / nuclear speck / cadherin binding / 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 ...: / 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
3-chloranyl-4-imidazol-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 / molecular replacement / Resolution: 1.4 Å
AuthorsWolter, M. / Dijck, L.v. / Ottmann, C.
Funding support2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179
H2020 Marie Curie Actions of the 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 10, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: 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)30,8268
Polymers30,4222
Non-polymers4046
Water6,125340
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)61,65316
Polymers60,8444
Non-polymers80912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5260 Å2
ΔGint-91 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.027, 111.940, 62.470
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-722-

HOH

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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: 28226.518 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, 346 molecules

#3: Chemical ChemComp-S6B / 3-chloranyl-4-imidazol-1-yl-benzaldehyde


Mass: 208.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9ClN2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.69 %
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: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.4→66.16 Å / Num. obs: 54952 / % possible obs: 96.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 15.67 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.014 / Rpim(I) all: 0.014 / Rrim(I) all: 0.02 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.421.90.241392420500.870.2410.3412.173.8
7.67-66.161.70.00767040410.0070.00941.899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12refinement
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AOG

7aog


Resolution: 1.4→55.97 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1823 2722 4.96 %
Rwork0.1655 100276 -
obs0.1664 54952 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.56 Å2 / Biso mean: 22.1579 Å2 / Biso min: 11.23 Å2
Refinement stepCycle: final / Resolution: 1.4→55.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 18 340 2258
Biso mean--26.21 32.77 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152105
X-RAY DIFFRACTIONf_angle_d1.3852862
X-RAY DIFFRACTIONf_chiral_restr0.087306
X-RAY DIFFRACTIONf_plane_restr0.008385
X-RAY DIFFRACTIONf_dihedral_angle_d10.0351207
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.41590.29121660.2659249771
1.4159-1.43260.23251200.2427254875
1.4326-1.450.26051630.2266273379
1.45-1.46840.1911180.206288783
1.4684-1.48770.25781320.1961314189
1.4877-1.50810.22821410.1873332894
1.5081-1.52970.21431890.18523428100
1.5297-1.55250.17611940.17953470100
1.5525-1.57670.22981770.17553451100
1.5767-1.60260.1781820.16063477100
1.6026-1.63020.18771710.17063420100
1.6302-1.65990.21491810.16793507100
1.6599-1.69180.20852240.173479100
1.6918-1.72630.20581420.17683460100
1.7263-1.76390.23731850.17123447100
1.7639-1.80490.19042040.16853441100
1.8049-1.85010.19211860.1623459100
1.8501-1.90010.17221610.16113511100
1.9001-1.9560.21311760.15923476100
1.956-2.01910.17631810.16713459100
2.0191-2.09130.17011660.15333484100
2.0913-2.1750.20391490.15383498100
2.175-2.2740.16781720.15343471100
2.274-2.39390.16372070.15313484100
2.3939-2.54390.18271850.16323407100
2.5439-2.74030.17631930.16693479100
2.7403-3.01610.17982370.17313424100
3.0161-3.45250.16381560.15823505100
3.4525-4.34950.15312320.14643398100
4.3495-55.970.19761460.17883507100

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