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- PDB-4u3z: APO MAP4K4 T181E Phosphomimetic Mutant -

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Basic information

Entry
Database: PDB / ID: 4u3z
TitleAPO MAP4K4 T181E Phosphomimetic Mutant
ComponentsMitogen-activated protein kinase kinase kinase kinase 4
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity ...positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity / MAPK cascade / microtubule binding / Oxidative Stress Induced Senescence / non-specific serine/threonine protein kinase / positive regulation of cell migration / intracellular signal transduction / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / ATP binding / cytoplasm
Similarity search - Function
Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / 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. ...Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / 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
Mitogen-activated protein kinase kinase kinase kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.09 Å
AuthorsHarris, S.F. / Wu, P. / Coons, M.
CitationJournal: to be published
Title: Structural Plasticity and Kinase Activation in a Cohort of MAP4K4 Structures
Authors: Wu, P. / Chen, H. / Coons, M. / Crawford, T.D. / Kirkpatrick, D.S. / Murray, L. / Ndubaku, C.O. / Nonomiya, J. / Pham, V. / Schmidt, S. / Smysczek, T. / Vitorino, P. / Ye, W. / Harris, S.F.
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Mitogen-activated protein kinase kinase kinase kinase 4
A: Mitogen-activated protein kinase kinase kinase kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2105
Polymers75,7962
Non-polymers4133
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-24 kcal/mol
Surface area27080 Å2
MethodPISA
2
B: Mitogen-activated protein kinase kinase kinase kinase 4


Theoretical massNumber of molelcules
Total (without water)37,8981
Polymers37,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Mitogen-activated protein kinase kinase kinase kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3124
Polymers37,8981
Non-polymers4133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.720, 80.900, 92.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase kinase 4 / HPK/GCK-like kinase HGK / MAPK/ERK kinase kinase kinase 4 / MEKKK 4 / Nck-interacting kinase


Mass: 37898.086 Da / Num. of mol.: 2 / Fragment: kinase domain (UNP residues 2-328) / Mutation: T181E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K4, HGK, KIAA0687, NIK / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: O95819, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 0.2 M potassium citrate, pH 8.3, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 15, 2013
RadiationMonochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.09→61 Å / Num. obs: 36129 / % possible obs: 100 % / Redundancy: 5.3 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.088 / Net I/σ(I): 11.2
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALAdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.6.4_486)refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.09→60.407 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1823 5.05 %
Rwork0.1826 34303 -
obs0.186 36126 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.429 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 109.7 Å2 / Biso mean: 36.1921 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1--4.109 Å2-0 Å20 Å2
2---1.3003 Å2-0 Å2
3---5.4093 Å2
Refinement stepCycle: final / Resolution: 2.09→60.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4673 0 25 411 5109
Biso mean--38.68 39.03 -
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074847
X-RAY DIFFRACTIONf_angle_d1.0816552
X-RAY DIFFRACTIONf_chiral_restr0.073705
X-RAY DIFFRACTIONf_plane_restr0.005838
X-RAY DIFFRACTIONf_dihedral_angle_d16.4261854
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.09-2.14650.28511380.222126112749
2.1465-2.20970.25451190.215226002719
2.2097-2.2810.29851420.198826032745
2.281-2.36250.28231450.19226092754
2.3625-2.45710.27281460.187825832729
2.4571-2.5690.27831440.188326212765
2.569-2.70440.29651340.185626142748
2.7044-2.87380.27631280.196926272755
2.8738-3.09570.2481450.197926372782
3.0957-3.40720.28411510.185526422793
3.4072-3.90020.24091410.164426472788
3.9002-4.91350.18391430.149127002843
4.9135-60.43230.23381470.192728092956

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