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- PDB-1ri9: Structure of a helically extended SH3 domain of the T cell adapte... -

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Basic information

Entry
Database: PDB / ID: 1ri9
TitleStructure of a helically extended SH3 domain of the T cell adapter protein ADAP
ComponentsFYN-binding protein
KeywordsSIGNALING PROTEIN / SH3-LIKE / HELICALLY EXTENDED
Function / homology
Function and homology information


anchoring junction / Signal regulatory protein family interactions / Generation of second messenger molecules / protein localization to plasma membrane / integrin-mediated signaling pathway / actin cytoskeleton / T cell receptor signaling pathway / immune response / signaling receptor binding / lipid binding ...anchoring junction / Signal regulatory protein family interactions / Generation of second messenger molecules / protein localization to plasma membrane / integrin-mediated signaling pathway / actin cytoskeleton / T cell receptor signaling pathway / immune response / signaling receptor binding / lipid binding / protein-containing complex binding / protein-containing complex / nucleus / plasma membrane / cytosol
Similarity search - Function
Helically-extended SH3 domain / FYB, helically extended SH3 domain / FYN-binding protein 1/2-like / Helically-extended SH3 domain / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...Helically-extended SH3 domain / FYB, helically extended SH3 domain / FYN-binding protein 1/2-like / Helically-extended SH3 domain / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
FYN-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHeuer, K. / Kofler, M. / Langdon, G. / Thiemke, K. / Freund, C.
CitationJournal: STRUCTURE / Year: 2004
Title: Structure of a Helically Extended SH3 Domain of the T Cell Adapter Protein ADAP.
Authors: Heuer, K. / Kofler, M. / Langdon, G. / Thiemke, K. / Freund, C.
History
DepositionNov 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FYN-binding protein


Theoretical massNumber of molelcules
Total (without water)11,9011
Polymers11,9011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 51The submitted conformer models are the 20 structures with the lowest energy.
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: Protein FYN-binding protein


Mass: 11901.391 Da / Num. of mol.: 1 / Fragment: RESIDUES 683-771 OF ADAP PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYB, SLAP130 / Plasmid: pTFT74 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O15117

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C-separated NOESY
1413D 15N-separated NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear and 3D heteronuclear techniques.

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Sample preparation

DetailsContents: 1.8mM ADAP-hSH3 domain "[U-95% 13C; U-90% 15N]" / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.05 / pH: 6.3 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker GmbHcollection
XEASY1.3.13Bartels, C., Xia, T.H., Billeter, M., Guentert, P. and Wuethrich, K.data analysis
CYANA1.0.6Guentert, P.structure solution
CYANA1.0.6Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1136 restraints, 718 are NOE-derived distance constraints, 388 dihedral angle restraints,30 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the lowest energy.
Conformers calculated total number: 51 / Conformers submitted total number: 20

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