[English] 日本語
Yorodumi
- PDB-6f08: 14-3-3 zeta in complex with the human Son of sevenless homolog 1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6f08
Title14-3-3 zeta in complex with the human Son of sevenless homolog 1 (SOS1)
Components
  • 14-3-3 protein zeta/delta
  • Son of sevenless homolog 1
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / SOS1 / dimer / phosphosite
Function / homology
Function and homology information


GTPase complex / synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / establishment of Golgi localization / tube formation / Rap1 signalling / Interleukin-15 signaling / regulation of synapse maturation ...GTPase complex / synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / establishment of Golgi localization / tube formation / Rap1 signalling / Interleukin-15 signaling / regulation of synapse maturation / Activation of RAC1 / neurotrophin TRK receptor signaling pathway / Signaling by LTK / leukocyte migration / negative regulation of protein localization to nucleus / Regulation of KIT signaling / epidermal growth factor receptor binding / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / NRAGE signals death through JNK / positive regulation of Rac protein signal transduction / Fc-epsilon receptor signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / lung development / RET signaling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Signal attenuation / regulation of ERK1 and ERK2 cascade / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Schwann cell development / SHC1 events in ERBB4 signaling / response to ischemia / Signalling to RAS / cellular response to glucose starvation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / myelination / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Erythropoietin activates RAS / insulin-like growth factor receptor signaling pathway / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / RAC1 GTPase cycle / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / Signaling by FGFR2 in disease / Transcriptional and post-translational regulation of MITF-M expression and activity / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / SHC1 events in EGFR signaling / FCERI mediated Ca+2 mobilization / FLT3 Signaling / EGFR Transactivation by Gastrin / Signaling by FGFR1 in disease / B cell receptor signaling pathway / NCAM signaling for neurite out-growth / GTPase activator activity / guanyl-nucleotide exchange factor activity / GRB2 events in ERBB2 signaling / negative regulation of innate immune response / axon guidance / Downstream signal transduction / negative regulation of TORC1 signaling / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / hippocampal mossy fiber to CA3 synapse / T cell activation / TP53 Regulates Metabolic Genes / FCERI mediated MAPK activation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / SH3 domain binding / regulation of protein stability / Signaling by ERBB2 TMD/JMD mutants / molecular condensate scaffold activity / Constitutive Signaling by EGFRvIII
Similarity search - Function
Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain ...Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / : / SOS1/NGEF-like PH domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / 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 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Histone-fold / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein zeta/delta / Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBallone, A. / Centorrino, F. / Ottmann, C. / Guo, S. / Leysen, S.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionGrant Agreement 675179 Netherlands
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Structural characterization of 14-3-3 zeta in complex with the human Son of sevenless homolog 1 (SOS1).
Authors: Ballone, A. / Centorrino, F. / Wolter, M. / Ottmann, C.
History
DepositionNov 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength
Revision 1.4Oct 9, 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 zeta/delta
B: 14-3-3 protein zeta/delta
D: Son of sevenless homolog 1
I: 14-3-3 protein zeta/delta
J: 14-3-3 protein zeta/delta
K: Son of sevenless homolog 1
N: Son of sevenless homolog 1
Q: Son of sevenless homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5959
Polymers111,3578
Non-polymers2381
Water12,484693
1
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
D: Son of sevenless homolog 1
Q: Son of sevenless homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9175
Polymers55,6794
Non-polymers2381
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-35 kcal/mol
Surface area21400 Å2
MethodPISA
2
I: 14-3-3 protein zeta/delta
J: 14-3-3 protein zeta/delta
K: Son of sevenless homolog 1
N: Son of sevenless homolog 1


Theoretical massNumber of molelcules
Total (without water)55,6794
Polymers55,6794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-32 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.059, 93.140, 74.519
Angle α, β, γ (deg.)90.00, 92.93, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 26316.764 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli (E. coli) / References: UniProt: P63104
#2: Protein/peptide
Son of sevenless homolog 1 / SOS-1


Mass: 1522.537 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07889
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M phosphate citrate pH 4.2, 36% (v/v) PEG 300

-
Data collection

DiffractionMean temperature: 193.15 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 2 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 1.9→74.42 Å / Num. obs: 68382 / % possible obs: 99.93 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.075 / Rrim(I) all: 0.135 / Net I/σ(I): 2.34
Reflection shellResolution: 1.9→1.949 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QJB

1qjb


Resolution: 1.9→74.42 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.894 / SU B: 4.791 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.175 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26732 3615 5 %RANDOM
Rwork0.21003 ---
obs0.21282 68382 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.173 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å2-0.08 Å2
2--1.78 Å2-0 Å2
3----1.11 Å2
Refinement stepCycle: 1 / Resolution: 1.9→74.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7110 0 16 693 7819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197214
X-RAY DIFFRACTIONr_bond_other_d0.0020.026538
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.9759734
X-RAY DIFFRACTIONr_angle_other_deg1.0853.00115099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2475906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24624.769325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.398151234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3311548
X-RAY DIFFRACTIONr_chiral_restr0.1040.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028021
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021413
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6122.6823682
X-RAY DIFFRACTIONr_mcbond_other2.612.6823681
X-RAY DIFFRACTIONr_mcangle_it3.8523.994572
X-RAY DIFFRACTIONr_mcangle_other3.8523.9914573
X-RAY DIFFRACTIONr_scbond_it3.0682.9143532
X-RAY DIFFRACTIONr_scbond_other3.0672.9143532
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6164.2595163
X-RAY DIFFRACTIONr_long_range_B_refined6.66332.7348710
X-RAY DIFFRACTIONr_long_range_B_other6.45332.2788513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 287 -
Rwork0.265 5011 -
obs--99.92 %

+
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