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- PDB-3mhr: 14-3-3 sigma in complex with YAP pS127-peptide -

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Basic information

Entry
Database: PDB / ID: 3mhr
Title14-3-3 sigma in complex with YAP pS127-peptide
Components
  • 14-3-3 protein sigma
  • YAP phosphopeptide
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / YAP / adapter protein / protein-protein interaction
Function / homology
Function and homology information


enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / tissue homeostasis / hippo signaling / regulation of stem cell proliferation / EGR2 and SOX10-mediated initiation of Schwann cell myelination / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / proline-rich region binding / Signaling by Hippo / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of epithelial cell differentiation / negative regulation of fat cell differentiation / organ growth / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / RUNX2 regulates osteoblast differentiation / progesterone receptor signaling pathway / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / regulation of neurogenesis / phosphoserine residue binding / canonical Wnt signaling pathway / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / positive regulation of osteoblast differentiation / vasculogenesis / Nuclear signaling by ERBB4 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / 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 / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / RHO GTPases activate PKNs / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / 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 / response to progesterone / epithelial cell proliferation / stem cell proliferation / positive regulation of epithelial cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / cellular response to gamma radiation / wound healing / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cell morphogenesis / positive regulation of protein localization to nucleus / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / intrinsic apoptotic signaling pathway in response to DNA damage / cell-cell junction / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / DNA-binding transcription factor binding / cell population proliferation / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / cadherin binding
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 proteins signature 2. ...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
14-3-3 protein sigma / Transcriptional coactivator YAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsSchumacher, B. / Skwarczynska, M. / Rose, R. / Ottmann, C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of a 14-3-3[sigma]-YAP phosphopeptide complex at 1.15 A resolution
Authors: Schumacher, B. / Skwarczynska, M. / Rose, R. / Ottmann, C.
History
DepositionApr 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3May 3, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: YAP phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,24914
Polymers27,6942
Non-polymers55512
Water5,188288
1
A: 14-3-3 protein sigma
P: YAP phosphopeptide
hetero molecules

A: 14-3-3 protein sigma
P: YAP phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,49928
Polymers55,3884
Non-polymers1,11124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area8240 Å2
ΔGint-174 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.270, 112.110, 62.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-233-

MG

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Components

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

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


Mass: 26558.914 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: GeneHogs DH10B / Gene: HME1, NM_006142, SFN / Plasmid: pPROEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P31947
#2: Protein/peptide YAP phosphopeptide


Mass: 1135.125 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence of the peptide occurs naturally in humans
Source: (synth.) Homo sapiens (human) / References: UniProt: P46937*PLUS

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Non-polymers , 5 types, 300 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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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: 52.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.095M HEPES Na-Salt pH7.4, 25.6% PEG 400, 0.19M CaCl2, 5% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.85 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.15→45.62 Å / Num. all: 103010 / Num. obs: 102833 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.31 % / Biso Wilson estimate: 14.083 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.54
Reflection shellResolution: 1.15→1.2 Å / Redundancy: 4.95 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 5.23 / Num. unique all: 12258 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ProDCdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3lw1

3lw1


Resolution: 1.15→45.62 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.681 / SU ML: 0.015 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15298 5142 5 %RANDOM
Rwork0.1265 ---
obs0.12779 97691 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.718 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.15→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 27 288 2241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222246
X-RAY DIFFRACTIONr_bond_other_d0.0020.021590
X-RAY DIFFRACTIONr_angle_refined_deg2.0551.9993084
X-RAY DIFFRACTIONr_angle_other_deg1.04233956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.8355.181332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22224.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08715.033455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7061515
X-RAY DIFFRACTIONr_chiral_restr0.1170.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02436
X-RAY DIFFRACTIONr_mcbond_it2.3331.51360
X-RAY DIFFRACTIONr_mcbond_other0.7751.5544
X-RAY DIFFRACTIONr_mcangle_it3.45722226
X-RAY DIFFRACTIONr_scbond_it5.3173886
X-RAY DIFFRACTIONr_scangle_it7.8214.5812
X-RAY DIFFRACTIONr_rigid_bond_restr2.18533836
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17 378 -
Rwork0.129 7175 -
obs--100 %

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