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- PDB-3vut: Crystal structures of non-phosphorylated MAP2K4 -

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Basic information

Entry
Database: PDB / ID: 3vut
TitleCrystal structures of non-phosphorylated MAP2K4
ComponentsDual specificity mitogen-activated protein kinase kinase 4
KeywordsTRANSFERASE / apo form / Kinase
Function / homology
Function and homology information


smooth muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / cellular response to sorbitol / JUN kinase kinase activity / cell growth involved in cardiac muscle cell development / mitogen-activated protein kinase kinase / negative regulation of motor neuron apoptotic process / positive regulation of nitric-oxide synthase biosynthetic process / Fc-epsilon receptor signaling pathway / Uptake and function of anthrax toxins ...smooth muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / cellular response to sorbitol / JUN kinase kinase activity / cell growth involved in cardiac muscle cell development / mitogen-activated protein kinase kinase / negative regulation of motor neuron apoptotic process / positive regulation of nitric-oxide synthase biosynthetic process / Fc-epsilon receptor signaling pathway / Uptake and function of anthrax toxins / JNK cascade / dendrite cytoplasm / MAP3K8 (TPL2)-dependent MAPK1/3 activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of DNA replication / FCERI mediated MAPK activation / positive regulation of JNK cascade / response to wounding / cellular response to mechanical stimulus / positive regulation of neuron apoptotic process / MAPK cascade / cellular senescence / perikaryon / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / molecular adaptor activity / protein kinase activity / positive regulation of protein phosphorylation / axon / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / cytosol
Similarity search - Function
Helix Hairpins - #2120 / Helix Hairpins / Helix non-globular / Special / 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. ...Helix Hairpins - #2120 / Helix Hairpins / Helix non-globular / Special / 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
Dual specificity mitogen-activated protein kinase kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsMatsumoto, T. / Kinoshita, T. / Kirii, Y. / Tada, T. / Yamano, A.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal and solution structures disclose a putative transient state of mitogen-activated protein kinase kinase 4
Authors: Matsumoto, T. / Kinoshita, T. / Kirii, Y. / Tada, T. / Yamano, A.
History
DepositionJul 5, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity mitogen-activated protein kinase kinase 4
B: Dual specificity mitogen-activated protein kinase kinase 4


Theoretical massNumber of molelcules
Total (without water)74,9422
Polymers74,9422
Non-polymers00
Water0
1
A: Dual specificity mitogen-activated protein kinase kinase 4


Theoretical massNumber of molelcules
Total (without water)37,4711
Polymers37,4711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity mitogen-activated protein kinase kinase 4


Theoretical massNumber of molelcules
Total (without water)37,4711
Polymers37,4711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.773, 87.362, 118.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dual specificity mitogen-activated protein kinase kinase 4 / MAP kinase kinase 4 / MAPKK 4 / JNK-activating kinase 1 / MAPK/ERK kinase 4 / MEK 4 / SAPK/ERK ...MAP kinase kinase 4 / MAPKK 4 / JNK-activating kinase 1 / MAPK/ERK kinase 4 / MEK 4 / SAPK/ERK kinase 1 / SEK1 / Stress-activated protein kinase kinase 1 / SAPK kinase 1 / SAPKK-1 / SAPKK1 / c-Jun N-terminal kinase kinase 1 / JNKK


Mass: 37470.996 Da / Num. of mol.: 2 / Fragment: UNP residues 80-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K4, JNKK1, MEK4, MKK4, PRKMK4, SEK1, SERK1, SKK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P45985, mitogen-activated protein kinase kinase

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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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium acetate, 22-25%(w/v) PEG3350, 0.1M HEPES-NaOH pH7.0, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 28, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→43 Å / Num. all: 9049 / Num. obs: 9049 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.068
Reflection shellResolution: 3.5→3.63 Å / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.6.0117refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.847 / Cor.coef. Fo:Fc free: 0.773 / SU B: 46.99 / SU ML: 0.733 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.40666 447 4.9 %RANDOM
Rwork0.3312 ---
all0.33471 8659 --
obs0.33471 8658 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 94.474 Å2
Baniso -1Baniso -2Baniso -3
1--2.97 Å2-0 Å2-0 Å2
2--1.78 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3457 0 0 0 3457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023512
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9894753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0035452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.52525.802131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.34415605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.53159
X-RAY DIFFRACTIONr_chiral_restr0.1160.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212554
LS refinement shellResolution: 3.498→3.586 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 40 -
Rwork0.263 600 -
obs--95.24 %

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