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- PDB-2lpe: Solution NMR Structure of the KSR1 CA1-CA1a domain -

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Basic information

Entry
Database: PDB / ID: 2lpe
TitleSolution NMR Structure of the KSR1 CA1-CA1a domain
ComponentsKinase suppressor of Ras 1
KeywordsSIGNALING PROTEIN / SAM DOMAIN / CC-SAM / COILED-COIL / SCAFFOLDING PROTEIN
Function / homology
Function and homology information


Negative regulation of MAPK pathway / RAF activation / MAP2K and MAPK activation / regulation of MAP kinase activity / MAP-kinase scaffold activity / mitogen-activated protein kinase kinase binding / 14-3-3 protein binding / cAMP-mediated signaling / Hsp90 protein binding / ruffle membrane ...Negative regulation of MAPK pathway / RAF activation / MAP2K and MAPK activation / regulation of MAP kinase activity / MAP-kinase scaffold activity / mitogen-activated protein kinase kinase binding / 14-3-3 protein binding / cAMP-mediated signaling / Hsp90 protein binding / ruffle membrane / regulation of cell population proliferation / protein-folding chaperone binding / Ras protein signal transduction / positive regulation of MAPK cascade / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein kinase binding / endoplasmic reticulum / protein-containing complex / ATP binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #1120 / SAM like domain present in kinase suppressor RAS 1 / Kinase suppressor RAS 1, N-terminal helical hairpin / Kinase suppressor RAS 1, N-terminal helical hairpin superfamily / Kinase suppressor RAS 1 N-terminal helical hairpin / Transcription Factor, Ets-1 / Zinc finger phorbol-ester/DAG-type signature. / Helix Hairpins / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) ...Helix Hairpins - #1120 / SAM like domain present in kinase suppressor RAS 1 / Kinase suppressor RAS 1, N-terminal helical hairpin / Kinase suppressor RAS 1, N-terminal helical hairpin superfamily / Kinase suppressor RAS 1 N-terminal helical hairpin / Transcription Factor, Ets-1 / Zinc finger phorbol-ester/DAG-type signature. / Helix Hairpins / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Sterile alpha motif/pointed domain superfamily / Helix non-globular / Special / DNA polymerase; domain 1 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Kinase suppressor of Ras 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / CNS water refinement using RECOORD scripts
Model detailslowest energy, model 1
AuthorsKoveal, D. / Peti, W. / Page, R.
CitationJournal: SCI.SIGNAL. / Year: 2012
Title: A CC-SAM, for Coiled Coil Sterile a Motif, Domain Targets the Scaffold KSR-1 to Specific Sites in the Plasma Membrane
Authors: Koveal, D. / Schuh-Nuhfer, N. / Ritt, D. / Page, R. / Morrison, D.K. / Peti, W.
History
DepositionFeb 11, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinase suppressor of Ras 1


Theoretical massNumber of molelcules
Total (without water)16,7211
Polymers16,7211
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Kinase suppressor of Ras 1 / mKSR1 / Protein Hb


Mass: 16721.152 Da / Num. of mol.: 1 / Fragment: UNP residues 25-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: DNA2.0 / Gene: Ksr, Ksr1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q61097

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-edited NOESY
1223D 13C-edited NOESY
1332D 1H-1H NOESY
1423D HNCA
1523D HN(CA)CB
1623D HBHA(CO)NH
1723D HNCO
1823D HN(CA)CO
1923D H(CCO)NH
11023D (H)CCH-TOCSY
11123D CBCA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-99% 15N] KSR1 CA1-CA1a domain, 20 mM sodium phosphate, 100 mM sodium chloride, 0.5 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-99% 13C; U-99% 15N] KSR1 CA1-CA1a domain, 20 mM sodium phosphate, 100 mM sodium chloride, 0.5 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
32 mM KSR1 CA1-CA1a domain, 20 mM sodium phosphate, 100 mM sodium chloride, 0.5 mM TCEP, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMKSR1 CA1-CA1a domain-1[U-99% 15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
0.5 mMTCEP-41
2 mMKSR1 CA1-CA1a domain-5[U-99% 13C; U-99% 15N]2
20 mMsodium phosphate-62
100 mMsodium chloride-72
0.5 mMTCEP-82
2 mMKSR1 CA1-CA1a domain-93
20 mMsodium phosphate-103
100 mMsodium chloride-113
0.5 mMTCEP-123
Sample conditionsIonic strength: 120 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger A. T. et.al.refinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
RefinementMethod: CNS water refinement using RECOORD scripts / Software ordinal: 1
NMR constraintsNOE constraints total: 3077 / NOE intraresidue total count: 422 / NOE long range total count: 1069 / NOE medium range total count: 779 / NOE sequential total count: 807
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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