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- PDB-2kym: Solution structure of the Bem1p SH3-CI domain from L.elongisporus... -

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Basic information

Entry
Database: PDB / ID: 2kym
TitleSolution structure of the Bem1p SH3-CI domain from L.elongisporus in complex with Ste20p peptide
Components
  • Bud emergence protein 1
  • Peptide form Serine/threonine-protein kinase STE20
KeywordsSIGNALING PROTEIN / SH3 domain / Bem1p / SH3-CI / Ste20p PRR / Cdc42p-interacting / scaffold
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 / bipolar cellular bud site selection / RHOD GTPase cycle / RHOV GTPase cycle / budding cell apical bud growth ...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 / bipolar cellular bud site selection / RHOD GTPase cycle / RHOV GTPase cycle / budding cell apical bud growth / RHOQ GTPase cycle / RHOU GTPase cycle / Regulation of actin dynamics for phagocytic cup formation / pseudohyphal growth / pheromone-dependent signal transduction involved in conjugation with cellular fusion / invasive growth in response to glucose limitation / vacuole inheritance / cellular bud site selection / incipient cellular bud site / regulation of exit from mitosis / mating projection tip / regulation of axonogenesis / MAPK6/MAPK4 signaling / regulation of MAPK cascade / stress granule assembly / phosphatidylinositol binding / cell morphogenesis / 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 / protein serine/threonine kinase activity / mRNA binding / negative regulation of transcription by RNA polymerase II / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Bem1/Scd2 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, PX domain / p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / PhoX homologous domain, present in p47phox and p40phox. ...Bem1/Scd2 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, PX domain / p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / 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
Uncharacterized protein / Serine/threonine-protein kinase STE20
Similarity search - Component
Biological speciesLodderomyces elongisporus (fungus)
Saccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsGorelik, M. / Muhandiram, R. / Davidson, A.R.
CitationJournal: To be Published
Title: Structural and functional characterization of an unusual SH3 domain from the fungal scaffold protein, Bem1p
Authors: Gorelik, M. / Muhandiram, R. / Yin, W. / Davidson, A.R.
History
DepositionJun 2, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bud emergence protein 1
B: Peptide form Serine/threonine-protein kinase STE20


Theoretical massNumber of molelcules
Total (without water)15,4122
Polymers15,4122
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
RepresentativeModel #1lowest energy

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Components

#1: Protein Bud emergence protein 1


Mass: 13772.495 Da / Num. of mol.: 1 / Fragment: SH3-CI domain, UNP residues 2-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lodderomyces elongisporus (fungus) / Strain: NRRL YB-4239 / Gene: LELG_04233 / Production host: Escherichia coli (E. coli) / References: UniProt: A5E3P5
#2: Protein/peptide Peptide form Serine/threonine-protein kinase STE20


Mass: 1639.915 Da / Num. of mol.: 1 / Fragment: PRR, UNP residues 468-483 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03497

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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 HNCO
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HNCA
1822D 1H-13C HSQC
1923D (H)CCH-TOCSY
11023D (H)CCH-COSY
11123D 1H-15N NOESY
11223D 1H-13C NOESY
113315N C13 filtered 2D 1H-1H TOCSY
114315N C13 filtered 2D 1H-1H NOESY
115415N C13 filtered 2D 1H-1H COSY
116413C half-filtered 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-99% 13C; U-99% 15N] Bem1 SH3-CI protein, 1.5 mM Ste20 peptide, 0.5 mM PMSF, 0.5 mM EDTA, 0.05 % sodium azide, 50 mM HEPES, 100 mM sodium chloride, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
20.7 mM [U-99% 13C; U-99% 15N] Bem1 SH3-CI protein, 1.5 mM Ste20 peptide, 0.5 mM PMSF, 0.5 mM EDTA, 0.05 % sodium azide, 50 mM HEPES, 100 mM sodium chloride, 1 mM DTT, 100% D2O100% D2O
30.5 mM [U-99% 13C; U-99% 15N] Bem1 SH3-CI protein, 0.5 mM Ste20 peptide, 100 mM sodium chloride, 50 mM sodium phosphate, 0.05 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
40.5 mM [U-99% 13C; U-99% 15N] Bem1 SH3-CI protein, 0.5 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 mMBem1 SH3-CI protein-1[U-99% 13C; U-99% 15N]1
1.5 mMSte20 peptide-21
0.5 mMPMSF-31
0.5 mMEDTA-41
0.05 %sodium azide-51
50 mMHEPES-61
100 mMsodium chloride-71
1 mMDTT-81
0.7 mMBem1 SH3-CI protein-9[U-99% 13C; U-99% 15N]2
1.5 mMSte20 peptide-102
0.5 mMPMSF-112
0.5 mMEDTA-122
0.05 %sodium azide-132
50 mMHEPES-142
100 mMsodium chloride-152
1 mMDTT-162
0.5 mMBem1 SH3-CI protein-17[U-99% 13C; U-99% 15N]3
0.5 mMSte20 peptide-183
100 mMsodium chloride-193
50 mMsodium phosphate-203
0.05 %sodium azide-213
0.5 mMBem1 SH3-CI protein-22[U-99% 13C; U-99% 15N]4
0.5 mMSte20 peptide-234
100 mMsodium chloride-244
50 mMsodium phosphate-254
0.05 %sodium azide-264
Sample conditionsIonic strength: 100 / pH: 6.8 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 71 / Protein psi angle constraints total count: 73
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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