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- PDB-7juu: Crystal Structure of KSR2:MEK1 in complex with AMP-PNP, and allos... -

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Basic information

Entry
Database: PDB / ID: 7juu
TitleCrystal Structure of KSR2:MEK1 in complex with AMP-PNP, and allosteric MEK inhibitor PD0325901
Components
  • Dual specificity mitogen-activated protein kinase kinase 1
  • Kinase suppressor of Ras 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / Pseudokinase / drug target / cell signaling and cancer / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


mitogen-activated protein kinase kinase / MAP-kinase scaffold activity / regulation of Golgi inheritance / mitogen-activated protein kinase kinase binding / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / MAP kinase kinase activity / calcium-mediated signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation ...mitogen-activated protein kinase kinase / MAP-kinase scaffold activity / regulation of Golgi inheritance / mitogen-activated protein kinase kinase binding / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / MAP kinase kinase activity / calcium-mediated signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / 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 / positive regulation of cold-induced thermogenesis / protein tyrosine kinase activity / Ras protein signal transduction / early endosome / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of MAPK cascade / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / centrosome / mitochondrion / zinc ion binding / ATP binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Kinase suppressor of RAS, SAM-like domain / 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 / : / : / 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) ...Kinase suppressor of RAS, SAM-like domain / 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 / : / : / 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. / 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
Chem-4BM / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Dual specificity mitogen-activated protein kinase kinase 1 / Kinase suppressor of Ras 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 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 1.1Dec 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 1.2Oct 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 2
C: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4117
Polymers82,8682
Non-polymers1,5435
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The MEK1:KSR2 heterodimer was also eluted as a homo-dimer of MEK1:KSR2 heterodimer, centered around KSR2
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-38 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.000, 140.000, 220.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 2 types, 2 molecules BC

#1: Protein Kinase suppressor of Ras 2 / hKSR2


Mass: 39748.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KSR2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6VAB6, 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

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Non-polymers , 4 types, 8 molecules

#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: Chemical ChemComp-4BM / N-{[(2R)-2,3-dihydroxypropyl]oxy}-3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]benzamide


Mass: 482.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14F3IN2O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.76 Å3/Da / Density % sol: 67.25 %
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: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 21556 / % possible obs: 99.8 % / Redundancy: 10.95 % / CC1/2: 0.999 / Net I/σ(I): 17.7
Reflection shellResolution: 3.19→3.27 Å / Num. unique obs: 1549 / CC1/2: 0.482

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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: 3.19→30.027 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 1138 5.28 %
Rwork0.241 --
obs0.242 21548 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.19→30.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 90 3 4738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034835
X-RAY DIFFRACTIONf_angle_d0.5746527
X-RAY DIFFRACTIONf_dihedral_angle_d9.8812905
X-RAY DIFFRACTIONf_chiral_restr0.042714
X-RAY DIFFRACTIONf_plane_restr0.004819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1902-3.33520.41351360.36582240X-RAY DIFFRACTION89
3.3352-3.51080.32681400.29972520X-RAY DIFFRACTION100
3.5108-3.73040.30951220.2892555X-RAY DIFFRACTION100
3.7304-4.01780.29431340.26292552X-RAY DIFFRACTION100
4.0178-4.4210.25671370.24622568X-RAY DIFFRACTION100
4.421-5.0581432586X-RAY DIFFRACTION100
5.058-6.36260.2641520.25542631X-RAY DIFFRACTION100
6.3626-30.0270.23551740.20212758X-RAY DIFFRACTION100

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