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- PDB-5n75: 14-3-3 sigma in complex with TAZ pS89 peptide -

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Basic information

Entry
Database: PDB / ID: 5n75
Title14-3-3 sigma in complex with TAZ pS89 peptide
Components
  • 14-3-3 protein sigma
  • WW domain-containing transcription regulator protein 1
KeywordsSIGNALING PROTEIN / 14-3-3 / TAZ / YAP
Function / homology
Function and homology information


kidney morphogenesis / regulation of metanephric nephron tubule epithelial cell differentiation / RUNX3 regulates YAP1-mediated transcription / Physiological factors / mesenchymal cell differentiation / heart process / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / tissue homeostasis / EGR2 and SOX10-mediated initiation of Schwann cell myelination ...kidney morphogenesis / regulation of metanephric nephron tubule epithelial cell differentiation / RUNX3 regulates YAP1-mediated transcription / Physiological factors / mesenchymal cell differentiation / heart process / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / tissue homeostasis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / SMAD protein signal transduction / glomerulus development / Signaling by Hippo / stem cell division / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / regulation of epidermal cell division / negative regulation of fat cell differentiation / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / RUNX2 regulates osteoblast differentiation / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / cilium assembly / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / bicellular tight junction / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / 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 / positive regulation of cell adhesion / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / transcription coregulator activity / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of canonical Wnt signaling pathway / positive regulation of protein localization to nucleus / multicellular organism growth / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / transcription corepressor activity / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / transcription regulator complex / transcription coactivator activity / regulation of cell cycle / protein ubiquitination / nuclear body / cadherin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
WW domain containing transcription regulator 1 / 14-3-3 protein sigma / WW domain-containing transcription regulator protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsSijbesma, E. / Leysen, S. / Ottmann, C.
CitationJournal: Biochemistry / Year: 2017
Title: Identification of Two Secondary Ligand Binding Sites in 14-3-3 Proteins Using Fragment Screening.
Authors: Sijbesma, E. / Skora, L. / Leysen, S. / Brunsveld, L. / Koch, U. / Nussbaumer, P. / Jahnke, W. / Ottmann, C.
History
DepositionFeb 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: WW domain-containing transcription regulator protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8738
Polymers27,6942
Non-polymers1796
Water4,630257
1
A: 14-3-3 protein sigma
P: WW domain-containing transcription regulator protein 1
hetero molecules

A: 14-3-3 protein sigma
P: WW domain-containing transcription regulator protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,74716
Polymers55,3884
Non-polymers35912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6630 Å2
ΔGint-120 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.176, 112.269, 62.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 26542.914 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 WW domain-containing transcription regulator protein 1 / TAZ pS89 peptide


Mass: 1151.125 Da / Num. of mol.: 1 / Fragment: UNP residues 86-95 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: C9JQS8, UniProt: Q9GZV5*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.095 M HEPES Na pH 7.1, 28% PEG400, 0.19M Calcium chloride, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→45.6 Å / Num. obs: 27105 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 11.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Net I/σ(I): 33.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.844.30.120.9890.0630.13694.5
9.01-45.64.50.01710.0080.01998.3

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHR

3mhr


Resolution: 1.803→34.386 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.42
RfactorNum. reflection% reflection
Rfree0.1859 1429 5.28 %
Rwork0.153 --
obs0.1547 27083 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.4 Å2 / Biso mean: 15.582 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 1.803→34.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 6 257 2185
Biso mean--27.2 20.99 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052094
X-RAY DIFFRACTIONf_angle_d0.7072836
X-RAY DIFFRACTIONf_chiral_restr0.036308
X-RAY DIFFRACTIONf_plane_restr0.004373
X-RAY DIFFRACTIONf_dihedral_angle_d17.8741351
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8026-1.8670.19861320.15632447257996
1.867-1.94180.19861290.15525382667100
1.9418-2.03010.20981360.14825672703100
2.0301-2.13710.19881360.14725362672100
2.1371-2.2710.19841290.13825742703100
2.271-2.44630.18051590.138125342693100
2.4463-2.69240.17391330.147325832716100
2.6924-3.08180.18891500.160925722722100
3.0818-3.88190.17341680.153325982766100
3.8819-34.39230.18121570.168427052862100

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