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- PDB-2csi: Solution structure of the third SH3 domain of human RIM-binding p... -

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Basic information

Entry
Database: PDB / ID: 2csi
TitleSolution structure of the third SH3 domain of human RIM-binding protein 2
ComponentsRIM binding protein 2
KeywordsENDOCYTOSIS/EXOCYTOSIS / SH3 domain / RIM binding protein 2 / RIM-BP2 / 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


neuromuscular synaptic transmission / synapse / plasma membrane
Similarity search - Function
RIMS-binding protein, second SH3 domain / RIMS-binding protein, third SH3 domain / RIMS-binding protein 1/2/3 / Variant SH3 domain / Variant SH3 domain / SH3 Domains / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III ...RIMS-binding protein, second SH3 domain / RIMS-binding protein, third SH3 domain / RIMS-binding protein 1/2/3 / Variant SH3 domain / Variant SH3 domain / SH3 Domains / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
RIMS-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsInoue, K. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Solution structure of the third SH3 domain of human RIM-binding protein 2
Authors: Inoue, K. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 21, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2005Provider: 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_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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIM binding protein 2


Theoretical massNumber of molelcules
Total (without water)8,1211
Polymers8,1211
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 RIM binding protein 2 / RIM-BP2


Mass: 8120.700 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: KAZUSA cDNA hg00364 / Plasmid: P040705-06 / References: UniProt: O15034

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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: 1.08mM U-15N, 13C-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / 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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