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- PDB-2lcs: Yeast Nbp2p SH3 domain in complex with a peptide from Ste20p -

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Basic information

Entry
Database: PDB / ID: 2lcs
TitleYeast Nbp2p SH3 domain in complex with a peptide from Ste20p
Components
  • NAP1-binding protein 2
  • Serine/threonine-protein kinase STE20
KeywordsTRANSFERASE / signaling protein / adaptor
Function / homology
Function and homology information


sterol import / histone H2BS14 kinase activity / CD28 dependent Vav1 pathway / : / osmosensory signaling pathway via Sho1 osmosensor / RHO GTPases activate PAKs / signal transduction involved in filamentous growth / Signal transduction by L1 / RHOU GTPase cycle / bipolar cellular bud site selection ...sterol import / histone H2BS14 kinase activity / CD28 dependent Vav1 pathway / : / osmosensory signaling pathway via Sho1 osmosensor / RHO GTPases activate PAKs / signal transduction involved in filamentous growth / Signal transduction by L1 / RHOU GTPase cycle / bipolar cellular bud site selection / RHOV GTPase cycle / RHOD GTPase cycle / RHOQ GTPase cycle / budding cell apical bud growth / pseudohyphal growth / pheromone-dependent signal transduction involved in conjugation with cellular fusion / Regulation of actin dynamics for phagocytic cup formation / vacuole inheritance / invasive growth in response to glucose limitation / cellular bud site selection / MAPK6/MAPK4 signaling / incipient cellular bud site / regulation of exit from mitosis / mating projection tip / negative regulation of MAPK cascade / regulation of MAPK cascade / stress granule assembly / protein-macromolecule adaptor activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / phosphorylation / negative regulation of gene expression / protein serine kinase activity / mRNA binding / protein serine/threonine kinase activity / negative regulation of transcription by RNA polymerase II / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. ...p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase STE20 / NAP1-binding protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsGorelik, M. / Davidson, A.R.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Distinct Peptide Binding Specificities of Src Homology 3 (SH3) Protein Domains Can Be Determined by Modulation of Local Energetics across the Binding Interface.
Authors: Gorelik, M. / Davidson, A.R.
History
DepositionMay 7, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references

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Structure visualization

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Assembly

Deposited unit
A: NAP1-binding protein 2
B: Serine/threonine-protein kinase STE20


Theoretical massNumber of molelcules
Total (without water)10,0312
Polymers10,0312
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 / 20target function
RepresentativeModel #1fewest violations

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Components

#1: Protein NAP1-binding protein 2


Mass: 8391.204 Da / Num. of mol.: 1 / Fragment: SH3 domain residues 110-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NBP2, YDR162C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12163
#2: Protein/peptide Serine/threonine-protein kinase STE20


Mass: 1639.915 Da / Num. of mol.: 1 / Fragment: sequence database residues 468-483 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast)
References: UniProt: Q03497, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HN(CO)CA
1613D C(CO)NH
1713D H(CCO)NH
1823D (H)CCH-COSY
1923D 1H-15N NOESY
11023D 1H-13C NOESY
1113N15 C13 filtered 2D 1H-1H TOCSY
112315N C13 filtered 2D 1H-1H NOESY
113413C half-filtered 3D 1H-13C NOESY
114413C filtered 2D 1H-1H COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-99% 13C; U-99% 15N] Nbp2 SH3, 1.4 mM Ste20 peptide, 100 mM sodium chloride, 50 mM sodium phosphate, 0.05% % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.7 mM [U-99% 13C; U-99% 15N] Nbp2 SH3, 1.4 mM Ste20 peptide, 100 mM sodium chloride, 50 mM sodium phosphate, 0.05 % sodium azide, 100% D2O100% D2O
30.7 mM [U-99% 13C; U-99% 15N] Nbp2 SH3, 0.7 mM Ste20 peptide, 100 mM sodium chloride, 50 mM sodium phosphate, 0.05 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
40.7 mM [U-99% 13C; U-99% 15N] Nbp2 SH3, 0.7 mM Ste20 peptide, 100 mM sodium chloride, 50 mM sodium phosphate, 0.05 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMNbp2 SH3-1[U-99% 13C; U-99% 15N]1
1.4 mMSte20 peptide-21
100 mMsodium chloride-31
50 mMsodium phosphate-41
0.05 %sodium azide-51
0.7 mMNbp2 SH3-6[U-99% 13C; U-99% 15N]2
1.4 mMSte20 peptide-72
100 mMsodium chloride-82
50 mMsodium phosphate-92
0.05 %sodium azide-102
0.7 mMNbp2 SH3-11[U-99% 13C; U-99% 15N]3
0.7 mMSte20 peptide-123
100 mMsodium chloride-133
50 mMsodium phosphate-143
0.05 %sodium azide-153
0.7 mMNbp2 SH3-16[U-99% 13C; U-99% 15N]4
0.7 mMSte20 peptide-174
100 mMsodium chloride-184
50 mMsodium phosphate-194
0.05 %sodium azide-204
Sample conditionsIonic strength: 100 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker INOVABrukerINOVA5001
Bruker INOVABrukerINOVA8002

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Processing

NMR software
NameDeveloperClassification
SPARKYGoddardpeak picking
SPARKYGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2018 / NOE intraresidue total count: 345 / NOE long range total count: 999 / NOE medium range total count: 257 / NOE sequential total count: 417 / Protein phi angle constraints total count: 44 / Protein psi angle constraints total count: 43
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.01 Å / Maximum torsion angle constraint violation: 1.42 ° / Maximum upper distance constraint violation: 0.2 Å

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