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- PDB-1q9c: Crystal Structure of the Histone domain of Son of Sevenless -

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Basic information

Entry
Database: PDB / ID: 1q9c
TitleCrystal Structure of the Histone domain of Son of Sevenless
ComponentsSon of sevenless protein
KeywordsSIGNALING PROTEIN / Histone fold / H2A / H2B
Function / homology
Function and homology information


midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling ...midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / blood vessel morphogenesis / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / epidermal growth factor receptor binding / leukocyte migration / NRAGE signals death through JNK / regulation of T cell proliferation / roof of mouth development / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / SOS-mediated signalling / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / Signalling to RAS / fibroblast growth factor receptor signaling pathway / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / RAC1 GTPase cycle / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / myelination / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / GTPase activator activity / Insulin receptor signalling cascade / molecular condensate scaffold activity / guanyl-nucleotide exchange factor activity / insulin-like growth factor receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to ischemia / FCERI mediated MAPK activation / axon guidance / B cell receptor signaling pathway / Signaling by ERBB2 TMD/JMD mutants / multicellular organism growth / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / SH3 domain binding / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / G alpha (12/13) signalling events / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / insulin receptor signaling pathway / regulation of cell population proliferation / RAF/MAP kinase cascade / Ras protein signal transduction / Potential therapeutics for SARS / protein heterodimerization activity / neuronal cell body
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 guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor 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 guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor 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 / Histone, subunit A / Histone, subunit A / 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. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Core histone H2A/H2B/H3/H4 / Histone-fold / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.21 Å
AuthorsSondermann, H. / Soisson, S.M. / Bar-Sagi, D. / Kuriyan, J.
CitationJournal: Structure / Year: 2003
Title: Tandem Histone Folds in the Structure of the N-terminal Segment of the Ras Activator Son of Sevenless
Authors: Sondermann, H. / Soisson, S.M. / Bar-Sagi, D. / Kuriyan, J.
History
DepositionAug 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE THE AUTHORS SEQUENCED THE ORIGINAL DNA, AND CONSISTENTLY FIND AN ALA AT POSITION 145. ...SEQUENCE THE AUTHORS SEQUENCED THE ORIGINAL DNA, AND CONSISTENTLY FIND AN ALA AT POSITION 145. ALSO, THE DENSITY FITS BETTER FOR AN ALA (COMPARED TO VAL). THE AUTHORS STATE THAT IN MOST OF THE SEQUENCES FROM OTHER SPECIES AND ISOFORMS, THIS POSITION IS AN ALA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Son of sevenless protein
B: Son of sevenless protein
C: Son of sevenless protein
D: Son of sevenless protein
E: Son of sevenless protein
F: Son of sevenless protein
G: Son of sevenless protein
H: Son of sevenless protein
I: Son of sevenless protein


Theoretical massNumber of molelcules
Total (without water)199,7189
Polymers199,7189
Non-polymers00
Water0
1
A: Son of sevenless protein


Theoretical massNumber of molelcules
Total (without water)22,1911
Polymers22,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Son of sevenless protein


Theoretical massNumber of molelcules
Total (without water)22,1911
Polymers22,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Son of sevenless protein


Theoretical massNumber of molelcules
Total (without water)22,1911
Polymers22,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Son of sevenless protein


Theoretical massNumber of molelcules
Total (without water)22,1911
Polymers22,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Son of sevenless protein


Theoretical massNumber of molelcules
Total (without water)22,1911
Polymers22,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Son of sevenless protein


Theoretical massNumber of molelcules
Total (without water)22,1911
Polymers22,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Son of sevenless protein


Theoretical massNumber of molelcules
Total (without water)22,1911
Polymers22,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Son of sevenless protein


Theoretical massNumber of molelcules
Total (without water)22,1911
Polymers22,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Son of sevenless protein


Theoretical massNumber of molelcules
Total (without water)22,1911
Polymers22,1911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.397, 109.199, 212.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Son of sevenless protein / / SOS-1


Mass: 22190.918 Da / Num. of mol.: 9 / Fragment: N-terminal Histone domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOS1 / Plasmid: pProExHTb / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q07889

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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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, L-proline, magnesium acetate, ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-20 mg/mlprotein1drop
24-12 %PEG33501reservoir
30.2 ML-proline1reservoir
40.1 Mmagnesium acetate1reservoir
55 %ethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 26, 2002 / Details: Double-crystal Si(111)
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.211→19.9 Å / Num. all: 36035 / Num. obs: 35294 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 68.3 Å2 / Rsym value: 0.066 / Net I/σ(I): 20.1
Reflection shellResolution: 3.21→3.31 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.4 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 99 Å / % possible obs: 99 % / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.88

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.21→19.9 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2436 7 %RANDOM
Rwork0.255 ---
all-36060 --
obs-34887 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.0817 Å2 / ksol: 0.204227 e/Å3
Displacement parametersBiso mean: 82.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.78 Å20 Å20 Å2
2---10.31 Å20 Å2
3---6.53 Å2
Refine analyzeLuzzati coordinate error free: 0.49 Å / Luzzati sigma a free: 0.66 Å
Refinement stepCycle: LAST / Resolution: 3.21→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12555 0 0 0 12555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 3.21→3.41 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 387 7.4 %
Rwork0.338 4838 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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