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- PDB-2lj0: The third SH3 domain of R85FL -

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Basic information

Entry
Database: PDB / ID: 2lj0
TitleThe third SH3 domain of R85FL
ComponentsSorbin and SH3 domain-containing protein 1
KeywordsSIGNALING PROTEIN / SH3 / R85FL / ponsin / CAP
Function / homology
Function and homology information


cell-substrate junction / zonula adherens / flotillin complex / focal adhesion assembly / stress fiber assembly / cell-substrate adhesion / Smooth Muscle Contraction / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / stress fiber ...cell-substrate junction / zonula adherens / flotillin complex / focal adhesion assembly / stress fiber assembly / cell-substrate adhesion / Smooth Muscle Contraction / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / stress fiber / positive regulation of insulin receptor signaling pathway / cytoskeletal protein binding / cell-matrix adhesion / positive regulation of protein localization to plasma membrane / adherens junction / positive regulation of glucose import / insulin receptor binding / nuclear matrix / cellular response to insulin stimulus / signaling receptor complex adaptor activity / insulin receptor signaling pathway / actin binding / membrane raft / focal adhesion / centrosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
c-Cbl associated protein, SH3 domain / c-Cbl associated protein, SH3 domain 1 / c-Cbl associated protein, SH3 domain 2 / SoHo domain / Sorbin homologous domain / SoHo domain profile. / Sorbin homologous domain / Variant SH3 domain / Variant SH3 domain / SH3 Domains ...c-Cbl associated protein, SH3 domain / c-Cbl associated protein, SH3 domain 1 / c-Cbl associated protein, SH3 domain 2 / SoHo domain / Sorbin homologous domain / SoHo domain profile. / Sorbin homologous domain / Variant SH3 domain / Variant SH3 domain / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Sorbin and SH3 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsJiang, Y. / Hu, H.
CitationJournal: To be Published
Title: Structure Basis for the Recognition of Ataxin-7 PRR with R85FL SH3 Domain
Authors: Jiang, Y. / Zhou, C. / Zhou, Z. / Hu, H.
History
DepositionSep 2, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorbin and SH3 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)7,5811
Polymers7,5811
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sorbin and SH3 domain-containing protein 1 / Ponsin / SH3 domain protein 5 / SH3P12 / c-Cbl-associated protein / CAP


Mass: 7581.335 Da / Num. of mol.: 1 / Fragment: third SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SORBS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BX66

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D H(CCO)NH
1713D HNHA
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 1mM [U-99% 13C; U-99% 15N] sodium phosphate-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: sodium phosphate-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.12 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1168 / NOE intraresidue total count: 513 / NOE long range total count: 307 / NOE medium range total count: 68 / NOE sequential total count: 280
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15 / Representative conformer: 1

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