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- PDB-2dbm: Solution structures of the SH3 domain of human SH3-containing GRB... -

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Basic information

Entry
Database: PDB / ID: 2dbm
TitleSolution structures of the SH3 domain of human SH3-containing GRB2-like protein 2
ComponentsSH3-containing GRB2-like protein 2
KeywordsTRANSFERASE / SIGNALING PROTEIN / EC 2.3.1.- / SH3 domain protein 2A / Endophilin 1 / EEN-B1 / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of blood-brain barrier permeability / synaptic vesicle uncoating / dendrite extension / Retrograde neurotrophin signalling / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / Recycling pathway of L1 / cellular response to brain-derived neurotrophic factor stimulus / MHC class II antigen presentation / InlB-mediated entry of Listeria monocytogenes into host cell ...negative regulation of blood-brain barrier permeability / synaptic vesicle uncoating / dendrite extension / Retrograde neurotrophin signalling / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / Recycling pathway of L1 / cellular response to brain-derived neurotrophic factor stimulus / MHC class II antigen presentation / InlB-mediated entry of Listeria monocytogenes into host cell / negative regulation of protein phosphorylation / central nervous system development / cell projection / EGFR downregulation / clathrin-coated endocytic vesicle membrane / Negative regulation of MET activity / neuron projection development / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / early endosome / Golgi membrane / negative regulation of gene expression / lipid binding / glutamatergic synapse / perinuclear region of cytoplasm / signal transduction / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Endophilin-A, SH3 domain / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / Src homology 3 domains / SH3 type barrels. ...Endophilin-A, SH3 domain / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structures of the SH3 domain of human SH3-containing GRB2-like protein 2
Authors: Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionDec 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2006Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH3-containing GRB2-like protein 2


Theoretical massNumber of molelcules
Total (without water)7,8811
Polymers7,8811
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)20 / 100target function, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein SH3-containing GRB2-like protein 2 / SH3 domain protein 2A / Endophilin 1 / EEN-B1


Mass: 7880.576 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: SH3GL2 / Plasmid: P050620-01
References: UniProt: Q99962, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1mM SH3 domain U-15N,13C; 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
XwinNMR3.5Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.932Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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