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- PDB-2o2o: Solution structure of domain B from human CIN85 PROTEIN -

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Basic information

Entry
Database: PDB / ID: 2o2o
TitleSolution structure of domain B from human CIN85 PROTEIN
ComponentsSH3-domain kinase-binding protein 1
KeywordsPROTEIN BINDING / SH3 / CIN85
Function / homology
Function and homology information


Reelin signalling pathway / positive regulation of B cell activation / endocytic vesicle / cytoskeleton organization / InlB-mediated entry of Listeria monocytogenes into host cell / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / EGFR downregulation / cytoplasmic vesicle membrane / Negative regulation of MET activity ...Reelin signalling pathway / positive regulation of B cell activation / endocytic vesicle / cytoskeleton organization / InlB-mediated entry of Listeria monocytogenes into host cell / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / EGFR downregulation / cytoplasmic vesicle membrane / Negative regulation of MET activity / SH3 domain binding / endocytosis / cell-cell junction / cell migration / Cargo recognition for clathrin-mediated endocytosis / cell-cell signaling / Clathrin-mediated endocytosis / regulation of cell shape / Potential therapeutics for SARS / cytoskeleton / neuron projection / focal adhesion / apoptotic process / synapse / ubiquitin protein ligase binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SH3 domain-containing kinase-binding protein 1, first SH3 domain / SH3 domain-containing kinase-binding protein 1, second SH3 domain / SH3 domain-containing kinase-binding protein 1, third 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 ...SH3 domain-containing kinase-binding protein 1, first SH3 domain / SH3 domain-containing kinase-binding protein 1, second SH3 domain / SH3 domain-containing kinase-binding protein 1, third 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
SH3 domain-containing kinase-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsAbabou, A. / Pfuhl, M. / Dikic, I. / Ladbury, J.E.
CitationJournal: To be Published
Title: Investigation of Domain B from Human Cin85 Protein: Structure, Dynamics and Proline-Rich Motif Binding
Authors: Ababou, A. / Pfuhl, M. / Dikic, I. / Ladbury, J.E.
History
DepositionNov 30, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
Revision 1.3Dec 27, 2023Group: 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: SH3-domain kinase-binding protein 1


Theoretical massNumber of molelcules
Total (without water)10,5051
Polymers10,5051
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)27 / 40structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein SH3-domain kinase-binding protein 1 / SH3-DOMAIN B / Cbl-interacting protein of 85 kDa / Human Src-family kinase-binding protein 1 / HSB- ...SH3-DOMAIN B / Cbl-interacting protein of 85 kDa / Human Src-family kinase-binding protein 1 / HSB-1 / CD2-binding protein 3 / CD2BP3


Mass: 10504.551 Da / Num. of mol.: 1 / Fragment: CIN85_B
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SH3KBP1, CIN85 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: Q96B97

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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: 1MM CIN85_B U-15N PHOSPHATE BUFFER; 1MM CIN85_B U-15N,13C; 20MM PHOSPHATE BUFFER; 1MM CIN85_B U-15N,13C; 20MM PHOSPHATE BUFFER
Sample conditionsIonic strength: 20mM PO4, 100mM NACL, 1mM EDTA, 2mM DTT, 0.01% NAN3
pH: 6.3 / 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
NameVersionDeveloperClassification
ARIA1.2NILGESrefinement
NMRPipe290302structure solution
ANSIG3.3structure solution
Azara2.6structure solution
ARIA1.2structure solution
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 40 / Conformers submitted total number: 27

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