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- PDB-2rpn: A crucial role for high intrinsic specificity in the function of ... -

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Basic information

Entry
Database: PDB / ID: 2rpn
TitleA crucial role for high intrinsic specificity in the function of yeast SH3 domains
Components
  • Actin-binding protein
  • Actin-regulating kinase 1
KeywordsSTRUCTURAL PROTEIN / SH3 domain / extended peptide / 3-10 helix / Acetylation / Actin-binding / Cytoplasm / Cytoskeleton / Phosphoprotein
Function / homology
Function and homology information


protein localization to actin cortical patch / site of polarized growth / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch assembly / regulation of clathrin-dependent endocytosis / actin cortical patch / regulation of actin filament polymerization / barbed-end actin filament capping / mating projection tip / cortical actin cytoskeleton ...protein localization to actin cortical patch / site of polarized growth / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch assembly / regulation of clathrin-dependent endocytosis / actin cortical patch / regulation of actin filament polymerization / barbed-end actin filament capping / mating projection tip / cortical actin cytoskeleton / actin filament organization / actin filament binding / cell cortex / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / cytoplasm
Similarity search - Function
Fungal actin-binding protein 1, second SH3 domain / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. ...Fungal actin-binding protein 1, second SH3 domain / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Actin-binding protein / Actin-regulating kinase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailsSolution structure of Abp1p SH3 doain complexed with peptide from Ark1p
AuthorsStollar, E.J. / Garcia, B. / Chong, A. / Forman-Kay, J. / Davidson, A.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p
Authors: Stollar, E.J. / Garcia, B. / Chong, P.A. / Rath, A. / Lin, H. / Forman-Kay, J.D. / Davidson, A.R.
History
DepositionJun 12, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: 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_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 1.3May 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: Actin-binding protein
B: Actin-regulating kinase 1


Theoretical massNumber of molelcules
Total (without water)8,7222
Polymers8,7222
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Actin-binding protein / Abp1p


Mass: 6734.160 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: P15891
#2: Protein/peptide Actin-regulating kinase 1


Mass: 1987.451 Da / Num. of mol.: 1 / Fragment: UNP residues 605-621
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: P53974
Sequence detailsTHE NUMBERING IS SEQUENTIALLY REDUCED IN CHAIN B.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of Abp1p SH3 domain complexed with peptide from Ark1p
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H COSY
1512D 1H-1H NOESY
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D HNCO
1913D (H)CCH-TOCSY
11013D 1H-15N TOCSY
1111HN-N RDC
1121HACAN
1131N-CO RDC
1141CA-HA RDC
1151CA-CO RDC
1161CA-CB RDC
11713J NC
11813J CC

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Sample preparation

DetailsContents: 50mM sodium phosphate; 100mM sodium chloride; 1mM sodium azide; 1mM EDTA; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMsodium phosphate1
100 mMsodium chloride1
1 mMsodium azide1
1 mMEDTA1
Sample conditionsIonic strength: 0.208 / pH: 7 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
MOLMOLKoradi, Billeter and Wuthrichsuperposition
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIALinge, O'Donoghue and Nilgesstructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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