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- PDB-1pms: PLECKSTRIN HOMOLOGY DOMAIN OF SON OF SEVENLESS 1 (SOS1) WITH GLYC... -

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Basic information

Entry
Database: PDB / ID: 1pms
TitlePLECKSTRIN HOMOLOGY DOMAIN OF SON OF SEVENLESS 1 (SOS1) WITH GLYCINE-SERINE ADDED TO THE N-TERMINUS, NMR, 20 STRUCTURES
ComponentsSOS 1
KeywordsSIGNAL TRANSDUCTION / PLECKSTRIN / SON OF SEVENLESS / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC1 events in ERBB4 signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / SHC-mediated cascade:FGFR2 / SHC-related events triggered by IGF1R ...Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC1 events in ERBB4 signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / SHC-mediated cascade:FGFR2 / SHC-related events triggered by IGF1R / SOS-mediated signalling / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates RAS signaling / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / Tie2 Signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Interleukin-15 signaling / FLT3 Signaling / NCAM signaling for neurite out-growth / Regulation of KIT signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Downstream signal transduction / Insulin receptor signalling cascade / FCERI mediated MAPK activation / lymphocyte homeostasis / Signal attenuation / NRAGE signals death through JNK / Signaling by SCF-KIT / RAC1 GTPase cycle / GRB2:SOS provides linkage to MAPK signaling for Integrins / FCERI mediated Ca+2 mobilization / RAF/MAP kinase cascade / Interleukin receptor SHC signaling / G alpha (12/13) signalling events / midbrain morphogenesis / regulation of pro-B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / RET signaling / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / blood vessel morphogenesis / DAP12 signaling / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / regulation of T cell proliferation / ERBB2-ERBB3 signaling pathway / roof of mouth development / eyelid development in camera-type eye / neurotrophin TRK receptor signaling pathway / B cell homeostasis / hair follicle development / fibroblast growth factor receptor signaling pathway / Schwann cell development / heart morphogenesis / myelination / guanyl-nucleotide exchange factor activity / insulin-like growth factor receptor signaling pathway / molecular condensate scaffold activity / response to ischemia / B cell receptor signaling pathway / epidermal growth factor receptor signaling pathway / multicellular organism growth / SH3 domain binding / insulin receptor signaling pathway / regulation of cell population proliferation / Ras protein signal transduction / protein heterodimerization activity / neuronal cell body / regulation of transcription by RNA polymerase II / plasma membrane / cytosol / cytoplasm
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 / 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. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Histone-fold / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Son of sevenless homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsKoshiba, S. / Kigawa, T. / Kim, J. / Shirouzu, M. / Bowtell, D. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 1997
Title: The solution structure of the pleckstrin homology domain of mouse Son-of-sevenless 1 (mSos1).
Authors: Koshiba, S. / Kigawa, T. / Kim, J.H. / Shirouzu, M. / Bowtell, D. / Yokoyama, S.
History
DepositionFeb 18, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SOS 1


Theoretical massNumber of molelcules
Total (without water)15,5721
Polymers15,5721
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

#1: Protein SOS 1 / SON OF SEVENLESS


Mass: 15571.882 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN / Mutation: INS(GS-Q433)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX-4T3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62245

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT WAS VIA A SIMULATED ANNEALING PROTOCOL USING NMR-DERIVED RESTRAINTS AND X-PLOR 3.1. RMSD BACKBONE HEAVY ATOMS (SECONDARY STRUCTURE ELEMENTS) 0.70 +/- 0.34; ALL HEAVY ATOMS ...Details: REFINEMENT WAS VIA A SIMULATED ANNEALING PROTOCOL USING NMR-DERIVED RESTRAINTS AND X-PLOR 3.1. RMSD BACKBONE HEAVY ATOMS (SECONDARY STRUCTURE ELEMENTS) 0.70 +/- 0.34; ALL HEAVY ATOMS (SECONDARY STRUCTURE ELEMENTS) 1.24 +/-0.35.
NMR ensembleConformers submitted total number: 20

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