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- PDB-6bd1: Complex of 14-3-3 theta with an IRSp53 peptide phosphorylated at S366 -

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Basic information

Entry
Database: PDB / ID: 6bd1
TitleComplex of 14-3-3 theta with an IRSp53 peptide phosphorylated at S366
Components
  • 14-3-3 protein theta
  • Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
KeywordsSIGNALING PROTEIN / phosphate binding protein / protein complex / cytoskeleton regulation / cell motility
Function / homology
Function and homology information


RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / neuron projection branch point / dendritic spine cytoplasm / negative regulation of monoatomic ion transmembrane transport / TP53 Regulates Metabolic Genes / actin crosslink formation / plasma membrane organization ...RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / neuron projection branch point / dendritic spine cytoplasm / negative regulation of monoatomic ion transmembrane transport / TP53 Regulates Metabolic Genes / actin crosslink formation / plasma membrane organization / cadherin binding involved in cell-cell adhesion / positive regulation of dendritic spine morphogenesis / cytoskeletal anchor activity / regulation of modification of postsynaptic actin cytoskeleton / protein localization to synapse / cellular response to L-glutamate / neuron projection terminus / proline-rich region binding / positive regulation of actin filament polymerization / small GTPase-mediated signal transduction / dendrite development / actin filament bundle assembly / CDC42 GTPase cycle / Regulation of localization of FOXO transcription factors / postsynaptic cytosol / excitatory synapse / positive regulation of excitatory postsynaptic potential / Activation of BAD and translocation to mitochondria / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / postsynaptic density, intracellular component / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / presynaptic cytosol / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / ruffle / 14-3-3 protein binding / RAC1 GTPase cycle / substantia nigra development / cellular response to epidermal growth factor stimulus / axonogenesis / dendritic shaft / secretory granule / transcription coregulator binding / PDZ domain binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / filopodium / adherens junction / TP53 Regulates Metabolic Genes / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / synaptic membrane / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / intracellular protein localization / insulin receptor signaling pathway / lamellipodium / regulation of cell shape / scaffold protein binding / microtubule / transmembrane transporter binding / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / neuronal cell body / synapse / glutamatergic synapse / signal transduction / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
14-3-3 theta / I-BAR domain containing protein IRSp53 / IRSp53, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / AH/BAR domain superfamily / Variant SH3 domain / 14-3-3 domain ...14-3-3 theta / I-BAR domain containing protein IRSp53 / IRSp53, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / AH/BAR domain superfamily / Variant SH3 domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 14-3-3 protein theta / 14-3-3 protein theta / BAR/IMD domain-containing adapter protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsKast, D.J. / Dominguez, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01 MH087950 United States
CitationJournal: Nat Commun / Year: 2019
Title: Mechanism of IRSp53 inhibition by 14-3-3.
Authors: Kast, D.J. / Dominguez, R.
History
DepositionOct 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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_asym_id / _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_asym_id / _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.ptnr1_symmetry / _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 16, 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 theta
B: 14-3-3 protein theta
C: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
D: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
E: 14-3-3 protein theta
F: 14-3-3 protein theta
G: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
H: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,38018
Polymers117,3008
Non-polymers1,08010
Water7,314406
1
A: 14-3-3 protein theta
B: 14-3-3 protein theta
C: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
D: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
hetero molecules


  • defined by author&software
  • Evidence: light scattering, Assembly has a determined mass of 58 kDa, consistent with the theoretical mass of 1 dimer of 14-3-3 and 2 singly-phosphorylated IRSp53 peptide., isothermal titration ...Evidence: light scattering, Assembly has a determined mass of 58 kDa, consistent with the theoretical mass of 1 dimer of 14-3-3 and 2 singly-phosphorylated IRSp53 peptide., isothermal titration calorimetry, Stoichiometry determined from ITC is consistent with 1 14-3-3 dimer binding to 2 phosphorylated IRSp53 peptides.
  • 59.1 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)59,1499
Polymers58,6504
Non-polymers4995
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-40 kcal/mol
Surface area22470 Å2
MethodPISA
2
E: 14-3-3 protein theta
F: 14-3-3 protein theta
G: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
H: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2319
Polymers58,6504
Non-polymers5815
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-27 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.916, 69.301, 84.732
Angle α, β, γ (deg.)106.110, 95.560, 114.870
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABEFCDGH

#1: Protein
14-3-3 protein theta


Mass: 27795.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTYB11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3SZI4, UniProt: P27348*PLUS
#2: Protein/peptide
Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)


Mass: 1529.652 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQB8*PLUS

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Non-polymers , 4 types, 416 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.125 M CaCl2, 12% Peg 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Feb 17, 2012 / Details: Quazar MX optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→29.421 Å / Num. obs: 45896 / % possible obs: 95.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 23.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 4330 / CC1/2: 0.889 / % possible all: 90.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PROTEUM2data collection
PROTEUM2data processing
SAINTdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BR9

2br9


Resolution: 2.35→29.421 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.07
RfactorNum. reflection% reflection
Rfree0.2513 1905 4.15 %
Rwork0.2119 --
obs0.2135 45857 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.36 Å2 / Biso mean: 34.944 Å2 / Biso min: 10.57 Å2
Refinement stepCycle: final / Resolution: 2.35→29.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7567 0 157 406 8130
Biso mean--44.79 29.89 -
Num. residues----946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027870
X-RAY DIFFRACTIONf_angle_d0.4510613
X-RAY DIFFRACTIONf_chiral_restr0.0321200
X-RAY DIFFRACTIONf_plane_restr0.0021360
X-RAY DIFFRACTIONf_dihedral_angle_d14.5264940
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.40880.33551290.29063042317191
2.4088-2.47390.30011350.24863084321994
2.4739-2.54660.25831360.23643051318794
2.5466-2.62880.25011320.23063096322894
2.6288-2.72270.28991340.23453158329295
2.7227-2.83160.26271360.23263122325895
2.8316-2.96030.2941360.22713110324695
2.9603-3.11620.2671370.22673180331796
3.1162-3.31120.29611330.24173166329996
3.3112-3.56650.24631400.21473152329296
3.5665-3.92470.22681380.19243170330897
3.9247-4.49090.22461400.17193179331997
4.4909-5.65140.21161410.17493222336398
5.6514-29.4230.21511380.19623220335898

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