[English] 日本語
Yorodumi
- PDB-6bd1: Complex of 14-3-3 theta with an IRSp53 peptide phosphorylated at S366 -

+
Open data


ID or keywords:

Loading...

-
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 / actin crosslink formation / plasma membrane organization / TP53 Regulates Metabolic Genes / negative regulation of monoatomic ion transmembrane transport ...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 / actin crosslink formation / plasma membrane organization / TP53 Regulates Metabolic Genes / negative regulation of monoatomic ion transmembrane transport / cadherin binding involved in cell-cell adhesion / cytoskeletal anchor activity / regulation of modification of postsynaptic actin cytoskeleton / positive regulation of dendritic spine morphogenesis / protein localization to synapse / neuron projection terminus / proline-rich region binding / cellular response to L-glutamate / small GTPase-mediated signal transduction / positive regulation of actin filament polymerization / dendrite development / actin filament bundle assembly / CDC42 GTPase cycle / Regulation of localization of FOXO transcription factors / excitatory synapse / Activation of BAD and translocation to mitochondria / RAC3 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / positive regulation of excitatory postsynaptic potential / postsynaptic cytosol / protein targeting / postsynaptic density, intracellular component / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / 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 / axonogenesis / secretory granule / cellular response to epidermal growth factor stimulus / synaptic membrane / dendritic shaft / transcription coregulator binding / TP53 Regulates Metabolic Genes / regulation of actin cytoskeleton organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / adherens junction / PDZ domain binding / filopodium / regulation of synaptic plasticity / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / Schaffer collateral - CA1 synapse / insulin receptor signaling pathway / intracellular protein localization / regulation of cell shape / lamellipodium / 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 / cytoplasm / cytosol
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more