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- PDB-7aqb: Crystal structure of human mitogen activated protein kinase 6 (MAPK6) -

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Basic information

Entry
Database: PDB / ID: 7aqb
TitleCrystal structure of human mitogen activated protein kinase 6 (MAPK6)
ComponentsMitogen-activated protein kinase 6
KeywordsTRANSFERASE / MAPK6 / ERK3 / Kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


septin cytoskeleton / positive regulation of dendritic spine development / MAP kinase activity / mitogen-activated protein kinase / MAPK6/MAPK4 signaling / intracellular signal transduction / cell cycle / protein heterodimerization activity / protein phosphorylation / protein serine kinase activity ...septin cytoskeleton / positive regulation of dendritic spine development / MAP kinase activity / mitogen-activated protein kinase / MAPK6/MAPK4 signaling / intracellular signal transduction / cell cycle / protein heterodimerization activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / signal transduction / protein-containing complex / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK3/4 / 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
Mitogen-activated protein kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsFilippakopoulos, P. / Schroeder, M. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Int J Mol Sci / Year: 2020
Title: Crystal Structure and Inhibitor Identifications Reveal Targeting Opportunity for the Atypical MAPK Kinase ERK3.
Authors: Schroder, M. / Filippakopoulos, P. / Schwalm, M.P. / Ferrer, C.A. / Drewry, D.H. / Knapp, S. / Chaikuad, A.
History
DepositionOct 20, 2020Deposition site: PDBE / Processing site: PDBE
SupersessionNov 11, 2020ID: 2I6L
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 6
B: Mitogen-activated protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6484
Polymers72,5622
Non-polymers862
Water1,38777
1
A: Mitogen-activated protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3052
Polymers36,2811
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3432
Polymers36,2811
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.317, 83.317, 181.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 21 - 320 / Label seq-ID: 14 - 313

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Mitogen-activated protein kinase 6 / MAPK 6 / Extracellular signal-regulated kinase 3 / ERK-3 / MAP kinase isoform p97 / p97-MAPK


Mass: 36280.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK6, ERK3, PRKM6 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q16659, mitogen-activated protein kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: 1.8M MgSO4; 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.25→48.88 Å / Num. obs: 31175 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.857 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.05 / Rrim(I) all: 0.164 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.25-2.3210.22.4842853828030.5620.8022.6132.1100
9-48.888.80.09852555940.8670.0410.10823.899.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1erk

1erk
PDB Unreleased entry


Resolution: 2.25→48.88 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 15.517 / SU ML: 0.181 / SU R Cruickshank DPI: 0.2934 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1564 5 %RANDOM
Rwork0.2224 ---
obs0.2242 29536 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.45 Å2 / Biso mean: 49.722 Å2 / Biso min: 20.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å2-0 Å2-0 Å2
2--1.59 Å2-0 Å2
3----3.18 Å2
Refinement stepCycle: final / Resolution: 2.25→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4123 0 5 77 4205
Biso mean--62.17 48.98 -
Num. residues----568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134212
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173928
X-RAY DIFFRACTIONr_angle_refined_deg1.461.635744
X-RAY DIFFRACTIONr_angle_other_deg1.2621.5678992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0785562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44124.014142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04415626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.995159
X-RAY DIFFRACTIONr_chiral_restr0.0640.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02841
Refine LS restraints NCS

Ens-ID: 1 / Number: 7266 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.25→2.309 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 85 -
Rwork0.291 2153 -
all-2238 -
obs--100 %
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)
11.16890.80860.73812.53721.2872.48090.02150.05970.18790.03290.03250.0928-0.1543-0.0173-0.0540.0242-0.00930.020.04720.01260.045632.86831.258723.6738
23.2237-0.4743-0.73542.2016-0.03422.4538-0.0965-0.0476-0.14140.03920.15820.11070.0805-0.2213-0.06170.05910.0387-0.02240.0647-0.00230.025357.7149-9.36545.8685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 320
2X-RAY DIFFRACTION2B21 - 401

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