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- PDB-2k9g: Solution structure of the third SH3 domain of the Cin85 adapter p... -

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Basic information

Entry
Database: PDB / ID: 2k9g
TitleSolution structure of the third SH3 domain of the Cin85 adapter protein
ComponentsSH3 domain-containing kinase-binding protein 1
KeywordsSIGNALING PROTEIN / Cin85 / SH3 / adaptor protein / downregulation / cbl / Apoptosis / Cell junction / Cytoplasmic vesicle / Cytoskeleton / Endocytosis / Membrane / Phosphoprotein / SH3 domain / SH3-binding / Synapse / Synaptosome
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 / distance geometry
AuthorsPhilippe, D.L. / Ladbury, J.E. / Pfuhl, M.
CitationJournal: To be Published
Title: Solution structure of the Sh3-C domain of Cin85
Authors: Philippe, D.L.
History
DepositionOct 10, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 domain-containing kinase-binding protein 1


Theoretical massNumber of molelcules
Total (without water)8,4791
Polymers8,4791
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 / 100structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

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


Mass: 8479.498 Da / Num. of mol.: 1 / Fragment: SH3 domain C, UNP residues 262-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIN85, SH3KBP1 / Plasmid: pLEICS-01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): BL21(DE3)star / References: UniProt: Q96B97

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1222D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1543D HN(CA)CB
1643D CBCA(CO)NH
1743D HNCA
1843D HNCO
1943D HCACO
11043D HBHA(CO)NH
11123D (H)CCH-TOCSY
11223D C(CO)NH
11343D HBHANH
11433D 1H-15N NOESY
11523D 1H-13C NOESY
11622D 1H-13C TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Cin85 SH3-C, 20mM sodium phosphate, 100mM sodium chloride, 1mM DTT, 1mM EDTA, 0.02% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21mM [U-98% 13C; U-98% 15N] Cin85 SH3-C, 20mM sodium phosphate, 100mM sodium chloride, 1mM DTT, 1mM EDTA, 0.02% sodium azide, 100% D2O100% D2O
31mM [U-99% 15N] Cin85 SH3-C, 20mM sodium phosphate, 100mM sodium chloride, 1mM DTT, 1mM EDTA, 0.02% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
41mM [U-99% 13C; U-99% 15N] Cin85 SH3-C, 20mM sodium phosphate, 100mM sodium chloride, 1mM DTT, 1mM EDTA, 0.02% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCin85 SH3-C1
20 mMsodium phosphate1
100 mMsodium chloride1
1 mMDTT1
1 mMEDTA1
0.02 %sodium azide1
1 mMCin85 SH3-C[U-98% 13C; U-98% 15N]2
20 mMsodium phosphate2
100 mMsodium chloride2
1 mMDTT2
1 mMEDTA2
0.02 %sodium azide2
1 mMCin85 SH3-C[U-99% 15N]3
20 mMsodium phosphate3
100 mMsodium chloride3
1 mMDTT3
1 mMEDTA3
0.02 %sodium azide3
1 mMCin85 SH3-C[U-99% 13C; U-99% 15N]4
20 mMsodium phosphate4
100 mMsodium chloride4
1 mMDTT4
1 mMEDTA4
0.02 %sodium azide4
Sample conditionsIonic strength: 140 / pH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE8004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3 to 2.1Bruker Biospincollection
TopSpin1.3 to 2.1Bruker Biospinprocessing
Analysis1.0.15CCPNpeak picking
Analysis1.0.15CCPNchemical shift assignment
Analysis1.0.15CCPNdata analysis
TALOSCornilescu, Delaglio, Baxdata analysis
CYANAGuntert, Mumenthaler, Wuthrichstructure solution
PSVSBhattacharya, Montelionedata analysis
WHAT IFVrienddata analysis
CYANAGuntert, Mumenthaler, Wuthrichrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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