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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 / Interleukin-15 signaling / Activation of RAC1 ...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 / Interleukin-15 signaling / Activation of RAC1 / positive regulation of small GTPase mediated signal transduction / Signaling by LTK / blood vessel morphogenesis / epidermal growth factor receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / leukocyte migration / NRAGE signals death through JNK / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / roof of mouth development / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / regulation of T cell proliferation / RET signaling / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / hair follicle development / 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 / SHC-mediated cascade:FGFR3 / 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 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / 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 / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / myelination / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / FCERI mediated Ca+2 mobilization / GRB2 events in ERBB2 signaling / Downstream signal transduction / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / GTPase activator activity / insulin-like growth factor receptor signaling pathway / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Constitutive Signaling by Overexpressed ERBB2 / T cell activation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / guanyl-nucleotide exchange factor activity / response to ischemia / B cell receptor signaling pathway / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / molecular condensate scaffold activity / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / cytokine-mediated signaling pathway / Signaling by ERBB2 ECD mutants / multicellular organism growth / Signaling by ERBB2 KD Mutants / SH3 domain binding / epidermal growth factor receptor signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / insulin receptor signaling pathway / DAP12 signaling / G alpha (12/13) signalling events / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / regulation of cell population proliferation / RAF/MAP kinase cascade / Potential therapeutics for SARS / Ras protein signal transduction
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 / 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. / Histone, subunit A / 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
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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

Downloads & links

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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
Water00
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
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: 2.71 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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