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- PDB-1kbf: Solution Structure of the Cysteine-Rich C1 Domain of Kinase Suppr... -

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Entry
Database: PDB / ID: 1kbf
TitleSolution Structure of the Cysteine-Rich C1 Domain of Kinase Suppressor of Ras
ComponentsKinase suppressor of Ras 1
KeywordsSIGNALING PROTEIN / Cysteine-rich domain / Zinc-binding protein
Function / homology
Function and homology information


Negative regulation of MAPK pathway / RAF activation / regulation of MAP kinase activity / MAP2K and MAPK activation / MAP-kinase scaffold activity / mitogen-activated protein kinase kinase binding / 14-3-3 protein binding / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity ...Negative regulation of MAPK pathway / RAF activation / regulation of MAP kinase activity / MAP2K and MAPK activation / MAP-kinase scaffold activity / mitogen-activated protein kinase kinase binding / 14-3-3 protein binding / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H3S10 kinase activity / AMP-activated protein kinase activity / histone H3T11 kinase activity / histone H3T3 kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T45 kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / Hsp90 protein binding / ruffle membrane / regulation of cell population proliferation / protein-folding chaperone binding / Ras protein signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of MAPK cascade / protein serine kinase activity / endoplasmic reticulum membrane / protein kinase binding / endoplasmic reticulum / protein-containing complex / zinc ion binding / ATP binding / membrane / cytosol
Similarity search - Function
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 / : / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Zinc finger phorbol-ester/DAG-type signature. / 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 ...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 / : / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Zinc finger phorbol-ester/DAG-type signature. / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Kinase suppressor of Ras 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics
AuthorsZhou, M. / Horita, D.A. / Waugh, D.S. / Byrd, R.A. / Morrison, D.K.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Solution structure and functional analysis of the cysteine-rich C1 domain of kinase suppressor of Ras (KSR).
Authors: Zhou, M. / Horita, D.A. / Waugh, D.S. / Byrd, R.A. / Morrison, D.K.
History
DepositionNov 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2019Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 2.0Feb 26, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / diffrn ...atom_site / diffrn / diffrn_radiation / diffrn_radiation_wavelength / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_torsion / pdbx_version / struct / struct_conn / struct_keywords / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.SG_entry / _pdbx_database_status.status_code_mr / _pdbx_nmr_exptl_sample_conditions.ionic_strength / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.sheet_id / _struct.pdbx_CASP_flag / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_keywords.text / _struct_ref_seq_dif.details / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Description: Model orientation/position / Provider: author / Type: Coordinate replacement
Revision 2.1Apr 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.2Oct 30, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinase suppressor of Ras 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7153
Polymers5,5841
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 5583.696 Da / Num. of mol.: 1 / Fragment: Cysteine-rich C1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ksr1, Ksr / Plasmid: pGEX-3X / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q61097, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1HSQC
121isotropic1HN(CA)CB
131isotropic1CBCA(CO)NH
141isotropic1C(CO)NH
151isotropic1HCCHTOCSY
171isotropic13D HNHB
161isotropic1HN(CO)HB
181isotropic23D 15N-edited NOESY-HSQC
1101isotropic213C and 15N-edited NOESY-HSQC
191isotropic23D 13C-edited NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] Kinase Suppressor of Ras, 30 mM Tris-acetate, 100 mM sodium chloride, 100 mM Na2SO4, 0.1 mM sodium citrate, 0.1 mM TCEP, 90% H2O/10% D2O
Label: sample1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMKinase Suppressor of Ras[U-100% 13C; U-100% 15N]1
30 mMTris-acetatenatural abundance1
100 mMsodium chloridenatural abundance1
100 mMNa2SO4natural abundance1
0.1 mMsodium citratenatural abundance1
0.1 mMTCEPnatural abundance1
Sample conditionsIonic strength: 100 mM NaCl Not defined / Label: cond1 / pH: 6.5 Not defined / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
ANSIG3.3Kraulisdata analysis
CNS1STEIN ET AL.refinement
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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