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- PDB-7juw: Crystal Structure of KSR1:MEK1 in complex with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 7juw
TitleCrystal Structure of KSR1:MEK1 in complex with AMP-PNP
Components
  • Dual specificity mitogen-activated protein kinase kinase 1
  • Kinase suppressor of Ras 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / Pseudokinase / drug target / cell signaling and cancer / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of MAP kinase activity / mitogen-activated protein kinase kinase / MAP-kinase scaffold activity / regulation of Golgi inheritance / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / MAP kinase kinase activity / cAMP-mediated signaling / 14-3-3 protein binding / RAF activation ...regulation of MAP kinase activity / mitogen-activated protein kinase kinase / MAP-kinase scaffold activity / regulation of Golgi inheritance / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / MAP kinase kinase activity / cAMP-mediated signaling / 14-3-3 protein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / ruffle membrane / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / late endosome / regulation of cell population proliferation / protein tyrosine kinase activity / Ras protein signal transduction / positive regulation of MAPK cascade / early endosome / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / focal adhesion / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / centrosome / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
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 / 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 / Protein tyrosine and serine/threonine kinase ...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 / 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 / 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. / 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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Dual specificity mitogen-activated protein kinase kinase 1 / Kinase suppressor of Ras 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsKhan, Z.M. / Dar, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)5R01CA227636-02 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)1DP2CA186570-01 United States
CitationJournal: Nature / Year: 2020
Title: Structural basis for the action of the drug trametinib at KSR-bound MEK.
Authors: Khan, Z.M. / Real, A.M. / Marsiglia, W.M. / Chow, A. / Duffy, M.E. / Yerabolu, J.R. / Scopton, A.P. / Dar, A.C.
History
DepositionAug 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 2.0Oct 7, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / entity_poly ...atom_site / entity_poly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_polymer_linkage / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_asym_id / _entity_poly.pdbx_strand_id ..._atom_site.auth_asym_id / _entity_poly.pdbx_strand_id / _pdbx_entry_details.compound_details / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_peptide_omega.auth_asym_id_1 / _pdbx_validate_peptide_omega.auth_asym_id_2 / _pdbx_validate_polymer_linkage.auth_asym_id_1 / _pdbx_validate_polymer_linkage.auth_asym_id_2 / _pdbx_validate_torsion.auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id
Revision 2.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Kinase suppressor of Ras 1
C: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7786
Polymers81,7172
Non-polymers1,0614
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The MEK1:KSR1 heterodimer was also eluted as a dimer of MEK1:KSR1 heterodimer, centered around KSR1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-45 kcal/mol
Surface area27350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.710, 137.710, 218.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Kinase suppressor of Ras 1


Mass: 38597.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KSR1, KSR / Plasmid: pFastBac Dual / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8IVT5, non-specific serine/threonine protein kinase
#2: Protein Dual specificity mitogen-activated protein kinase kinase 1 / MAPKK 1 / ERK activator kinase 1 / MAPK/ERK kinase 1 / MEK 1


Mass: 43119.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: MAP2K1, MEK1, PRKMK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P29678, mitogen-activated protein kinase kinase
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe author states that kinase suppressor of Ras 1 chain B is proteolytically cleaved between Trp632 ...The author states that kinase suppressor of Ras 1 chain B is proteolytically cleaved between Trp632 and His633.
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 72.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 2000, MES pH 6.5, Magnesium Acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→46.174 Å / Num. obs: 28363 / % possible obs: 99.4 % / Redundancy: 14.83 % / CC1/2: 0.99 / Net I/σ(I): 18.75
Reflection shellResolution: 2.88→2.95 Å / Num. unique obs: 2050 / CC1/2: 0.512

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y4I

2y4i


Resolution: 2.88→46.174 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2859 1423 5.03 %
Rwork0.2432 --
obs0.2453 28300 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.88→46.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4679 0 64 8 4751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064845
X-RAY DIFFRACTIONf_angle_d1.0026544
X-RAY DIFFRACTIONf_dihedral_angle_d8.7652910
X-RAY DIFFRACTIONf_chiral_restr0.055711
X-RAY DIFFRACTIONf_plane_restr0.006829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.98290.41161190.36062659X-RAY DIFFRACTION100
2.9829-3.10230.38391480.33922616X-RAY DIFFRACTION100
3.1023-3.24350.37121630.33062625X-RAY DIFFRACTION100
3.2435-3.41440.35321300.31352673X-RAY DIFFRACTION100
3.4144-3.62830.34441350.27692674X-RAY DIFFRACTION100
3.6283-3.90830.28051350.26722665X-RAY DIFFRACTION100
3.9083-4.30140.28461510.24272664X-RAY DIFFRACTION99
4.3014-4.92320.30831460.22042684X-RAY DIFFRACTION99
4.9232-6.20030.34911440.24782722X-RAY DIFFRACTION99
6.2003-100.21520.22895X-RAY DIFFRACTION99

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