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- PDB-2e8m: Solution structure of the C-terminal SAM-domain of epidermal grow... -

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Basic information

Entry
Database: PDB / ID: 2e8m
TitleSolution structure of the C-terminal SAM-domain of epidermal growth receptor pathway substrate 8
ComponentsEpidermal growth factor receptor kinase substrate 8
KeywordsSIGNALING PROTEIN / CELL-FREE PROTEIN SYNTHESIS / PROTEIN REGULATION / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of actin filament length / actin polymerization-dependent cell motility / dendritic cell migration / stereocilium tip / actin crosslink formation / behavioral response to ethanol / stereocilium / regulation of Rho protein signal transduction / barbed-end actin filament capping / Sensory processing of sound by outer hair cells of the cochlea ...regulation of actin filament length / actin polymerization-dependent cell motility / dendritic cell migration / stereocilium tip / actin crosslink formation / behavioral response to ethanol / stereocilium / regulation of Rho protein signal transduction / barbed-end actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of ruffle assembly / NMDA selective glutamate receptor complex / Sensory processing of sound by inner hair cells of the cochlea / exit from mitosis / Rac protein signal transduction / regulation of postsynaptic membrane neurotransmitter receptor levels / brush border / actin filament bundle assembly / Rho protein signal transduction / adult locomotory behavior / cellular response to leukemia inhibitory factor / small GTPase binding / ruffle membrane / actin binding / cell cortex / regulation of cell shape / growth cone / vesicle / postsynaptic density / glutamatergic synapse / extracellular exosome / plasma membrane
Similarity search - Function
Epidermal growth factor receptor kinase substrate, phosphotyrosine-binding domain / Eps8, SH3 domain / Epidermal growth factor receptor kinase substrate 8-like / SAM domain / SAM domain (Sterile alpha motif) / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Transcription Factor, Ets-1 / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain ...Epidermal growth factor receptor kinase substrate, phosphotyrosine-binding domain / Eps8, SH3 domain / Epidermal growth factor receptor kinase substrate 8-like / SAM domain / SAM domain (Sterile alpha motif) / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Transcription Factor, Ets-1 / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Sterile alpha motif/pointed domain superfamily / SH3 domain / Src homology 3 domains / DNA polymerase; domain 1 / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Epidermal growth factor receptor kinase substrate 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGoroncy, A.K. / Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the C-terminal SAM-domain of epidermal growth receptor pathway substrate 8
Authors: Goroncy, A.K. / Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionJan 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 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: Epidermal growth factor receptor kinase substrate 8


Theoretical massNumber of molelcules
Total (without water)10,4591
Polymers10,4591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Epidermal growth factor receptor kinase substrate 8 / epidermal growth receptor pathway substrate 8


Mass: 10458.687 Da / Num. of mol.: 1 / Fragment: SAM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: EPS8 / Plasmid: P050613-05 / References: UniProt: Q12929

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.04mM SAM DOMAIN, 20mM d-TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: AMBIENT / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P.GUNTERT ET AL.refinement
CYANA2.1P.GUNTERT ET AL.structure solution
XwinNMR3.5BRUKERcollection
NMRPipe2003112FRANK DELAGLIOprocessing
NMRView5.0.4BRUCE A. JOHNSONdata analysis
KUJIRA0.899aNAOHIRO KOBAYASHIdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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