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- PDB-1x43: Solution structure of the SH3 domain of Endophilin B1 (Sh3g1b1) -

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Basic information

Entry
Database: PDB / ID: 1x43
TitleSolution structure of the SH3 domain of Endophilin B1 (Sh3g1b1)
ComponentsSH3 domain GRB2-like protein B1
KeywordsENDOCYTOSIS/EXOCYTOSIS / SH3 domain / GRB2-like protein B1 / Endophilin B1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


lysophosphatidic acid acyltransferase activity / 'de novo' post-translational protein folding / : / protein localization to vacuolar membrane / : / positive regulation of neurotrophin TRK receptor signaling pathway / positive regulation of membrane tubulation / phosphatidic acid biosynthetic process / autophagic cell death / phospholipid biosynthetic process ...lysophosphatidic acid acyltransferase activity / 'de novo' post-translational protein folding / : / protein localization to vacuolar membrane / : / positive regulation of neurotrophin TRK receptor signaling pathway / positive regulation of membrane tubulation / phosphatidic acid biosynthetic process / autophagic cell death / phospholipid biosynthetic process / positive regulation of autophagosome assembly / receptor catabolic process / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / membrane fission / positive regulation of dendrite extension / mitochondrial envelope / positive regulation of dendrite morphogenesis / regulation of early endosome to late endosome transport / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / autophagosome membrane / cellular response to glucose starvation / positive regulation of autophagy / cellular response to amino acid starvation / mitochondrion organization / regulation of cytokinesis / fatty acid binding / positive regulation of protein-containing complex assembly / synaptic vesicle / midbody / mitochondrial outer membrane / early endosome / neuron projection / Golgi membrane / neuronal cell body / apoptotic process / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Endophilin-B1 / Endophilin-B1, BAR domain / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / SH3 type barrels. ...Endophilin-B1 / Endophilin-B1, BAR domain / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / 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
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQin, X.-R. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Solution structure of the SH3 domain of Endophilin B1 (Sh3g1b1)
Authors: Qin, X.-R. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _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

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH3 domain GRB2-like protein B1


Theoretical massNumber of molelcules
Total (without water)8,6201
Polymers8,6201
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 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein SH3 domain GRB2-like protein B1 / Endophilin B1


Mass: 8620.460 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell free protein synthesis / Gene: RIKEN cDNA library 4930422M04 / Plasmid: P041220-01
References: UniProt: Q9JK48, 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 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.52mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio,F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.9296Kobayashi,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 lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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