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- PDB-6f08: 14-3-3 zeta in complex with the human Son of sevenless homolog 1 ... -

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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


synaptic target recognition / Golgi reassembly / midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / heart trabecula morphogenesis ...synaptic target recognition / Golgi reassembly / midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / heart trabecula morphogenesis / respiratory system process / regulation of synapse maturation / tube formation / Rap1 signalling / regulation of T cell differentiation in thymus / GTPase complex / Interleukin-15 signaling / positive regulation of small GTPase mediated signal transduction / Activation of RAC1 / negative regulation of protein localization to nucleus / Signaling by LTK / blood vessel morphogenesis / epidermal growth factor receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / KSRP (KHSRP) binds and destabilizes mRNA / leukocyte migration / GP1b-IX-V activation signalling / NRAGE signals death through JNK / roof of mouth development / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / neurotrophin TRK receptor signaling pathway / B cell homeostasis / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of T cell proliferation / Regulation of localization of FOXO transcription factors / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / hair follicle development / Activation of BAD and translocation to mitochondria / SHC1 events in ERBB4 signaling / fibroblast growth factor receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / Signalling to RAS / Interleukin receptor SHC signaling / Signal attenuation / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SHC-mediated cascade:FGFR3 / regulation of ERK1 and ERK2 cascade / MET activates RAS signaling / Schwann cell development / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / cellular response to glucose starvation / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / FRS-mediated FGFR1 signaling / negative regulation of TORC1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / protein sequestering activity / Signaling by FGFR1 in disease / myelination / ERK1 and ERK2 cascade / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / FCERI mediated Ca+2 mobilization / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / GTPase activator activity / negative regulation of innate immune response / insulin-like growth factor receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / axon guidance
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 2.08 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

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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

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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 %

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