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- PDB-2y4i: KSR2-MEK1 heterodimer -

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Basic information

Entry
Database: PDB / ID: 2y4i
TitleKSR2-MEK1 heterodimer
Components
  • DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1
  • KINASE SUPPRESSOR OF RAS 2
KeywordsTRANSFERASE / KSR1
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 / positive regulation of MAPK cascade / early endosome / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / centrosome / mitochondrion / ATP binding / membrane / nucleus / metal ion binding / 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) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 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: 3.46 Å
AuthorsBrennan, D.F. / Barford, D.
CitationJournal: Nature / Year: 2011
Title: A Raf-Induced Allosteric Transition of Ksr Stimulates Ksr and Raf Phosphorylation of Mek
Authors: Brennan, D.F. / Dar, A.C. / Hertz, N.T. / Chao, W. / Burlingame, A.L. / Shokat, K.M. / Barford, D.
History
DepositionJan 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 25, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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 / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)81,5457
Polymers80,4472
Non-polymers1,0985
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-44.1 kcal/mol
Surface area29020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.565, 130.565, 221.005
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 2 / KSR2 / HKSR2


Mass: 36800.594 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 634-950
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21 / References: UniProt: Q6VAB6
#2: Protein DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 / MEK1 / MAP KINASE KINASE 1 / MAPKK 1 / ERK ACTIVATOR KINASE 1 / MAPK/ERK KINASE 1 / MEK 1


Mass: 43646.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYCTOLAGUS CUNICULUS (rabbit) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21
References: UniProt: P29678, mitogen-activated protein kinase kinase
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 3.44 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 12% (W/V) PEG 3350, 0.2 M NA CITRATE, 10 MM PR ACETATE, BIS-TRIS PROPANE PH 6.25.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.02
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. obs: 25175 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 120.95 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.5
Reflection shellResolution: 3.45→3.65 Å / Redundancy: 4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1S9J, 2P55, 1UWH, AND 3C4C

1s9j

2p55

1uwh

3c4c


Resolution: 3.46→39.86 Å / SU ML: 2.43 / σ(F): 0.03 / Phase error: 28.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2934 1259 5 %
Rwork0.2295 --
obs0.2327 25175 91.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 110 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.46→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 65 0 4661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034757
X-RAY DIFFRACTIONf_angle_d0.7296423
X-RAY DIFFRACTIONf_dihedral_angle_d13.0481777
X-RAY DIFFRACTIONf_chiral_restr0.046704
X-RAY DIFFRACTIONf_plane_restr0.003807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4574-3.59580.3751110.33862327X-RAY DIFFRACTION79
3.5958-3.75930.3821740.32712319X-RAY DIFFRACTION82
3.7593-3.95730.2921200.25732519X-RAY DIFFRACTION86
3.9573-4.2050.28941640.20972640X-RAY DIFFRACTION92
4.205-4.52930.2921540.19652769X-RAY DIFFRACTION96
4.5293-4.98430.26561490.20052824X-RAY DIFFRACTION97
4.9843-5.70370.27561200.21562842X-RAY DIFFRACTION96
5.7037-7.17920.3081290.22772820X-RAY DIFFRACTION97
7.1792-39.86270.2491380.20722856X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.90970.357-0.30934.62542.1360.64940.03730.3742-0.15980.2537-0.0078-0.01290.08670.50080.05361.19770.21430.19281.54180.36351.0112-9.637468.5555-11.3753
23.1605-4.4552-3.27981.92965.14783.75681.10683.46693.28721.63681.1366-0.29322.03192.8976-1.85671.04590.76870.05061.9790.30291.502-22.787951.566-9.9732
30.17362.4196-1.14751.4059-0.75843.95260.20650.0749-0.1817-0.02780.30550.23910.0332-1.2063-0.25490.93710.12570.36141.52210.41691.0148-25.659162.88751.2456
41.35920.20590.85221.75340.09242.1047-0.0854-0.2835-0.02560.0203-0.06291.4637-0.5654-0.5596-0.37791.7480.34570.63271.6910.6261.9143-27.945177.62535.4844
53.4395-3.4361.96012.5607-0.70811.9570.02850.2661-0.7113-0.7573-0.5616-0.64590.17820.92670.44671.5889-0.08870.17442.1470.25841.8433-9.270429.43219.33
64.73762.0481-1.83053.4405-0.21343.292-0.7815-0.647-0.32160.35950.4427-1.1277-0.0750.44220.3231.07030.16480.18330.95650.22511.41-22.421234.787610.6446
79.14521.81645.67071.75983.39819.28820.60961.90350.75860.3841-0.1836-0.06371.0583-2.8391-0.24441.8373-1.1704-0.52015.32741.15822.0243-29.620548.280219.1718
83.521-3.91055.02223.416-5.58029.4535-0.32890.54971.2719-0.4574-0.2159-0.77590.0672-0.11370.43571.0529-0.02150.07151.03090.25441.1384-41.345737.20722.2664
94.0183-0.8228-2.68674.11613.43141.7582-0.13030.1521-0.80620.7145-0.22730.93990.3695-0.12790.27111.4568-0.1712-0.03391.43470.25791.6432-40.124233.826811.8889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN B AND RESID 655:806)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 807:822)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 823:890)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 891:935)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 37:113)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 114:237)
7X-RAY DIFFRACTION7(CHAIN C AND RESID 238:242)
8X-RAY DIFFRACTION8(CHAIN C AND RESID 243:308)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 309:382)

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