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- PDB-4u3y: Apo Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) -

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Basic information

Entry
Database: PDB / ID: 4u3y
TitleApo Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4)
ComponentsMitogen-activated protein kinase kinase kinase kinase 4
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


positive regulation of ARF protein signal transduction / MAP kinase kinase kinase kinase activity / creatine kinase activity / positive regulation of hippo signaling / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / regulation of MAPK cascade / positive regulation of focal adhesion assembly / regulation of JNK cascade ...positive regulation of ARF protein signal transduction / MAP kinase kinase kinase kinase activity / creatine kinase activity / positive regulation of hippo signaling / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / regulation of MAPK cascade / positive regulation of focal adhesion assembly / 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 / intracellular signal transduction / positive regulation of cell migration / protein phosphorylation / protein serine kinase activity / focal adhesion / 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 / CNH domain / Citron homology (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 ...: / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (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: 1.45 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
A: Mitogen-activated protein kinase kinase kinase kinase 4
B: Mitogen-activated protein kinase kinase kinase kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8183
Polymers75,7402
Non-polymers781
Water12,034668
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-13 kcal/mol
Surface area25720 Å2
MethodPISA
2
A: Mitogen-activated protein kinase kinase kinase kinase 4


Theoretical massNumber of molelcules
Total (without water)37,8701
Polymers37,8701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Mitogen-activated protein kinase kinase kinase kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9482
Polymers37,8701
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.407, 80.839, 92.953
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: 37870.078 Da / Num. of mol.: 2 / Fragment: kinase domain (UNP residues 2-328)
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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 1.99 Å3/Da / Density % sol: 38.32 %
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: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2010
RadiationMonochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 108043 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 17.86 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.183 / Net I/av σ(I): 29.727 / Net I/σ(I): 12.7 / Num. measured all: 779291
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2
1.45-1.57.20.741107001.057
1.5-1.567.20.532106631.131
1.56-1.637.20.398106931.211
1.63-1.727.30.297107171.299
1.72-1.837.30.203107341.403
1.83-1.977.30.135107601.43
1.97-2.177.20.096107791.357
2.17-2.487.20.076108061.144
2.48-3.1270.046109230.96
3.12-307.30.029112680.852

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
BUSTER2.11.4refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→28.93 Å / Cor.coef. Fo:Fc: 0.9617 / Cor.coef. Fo:Fc free: 0.9529 / SU R Cruickshank DPI: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.068
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 5385 5 %RANDOM
Rwork0.1826 ---
obs0.1838 107719 99.99 %-
Displacement parametersBiso max: 124.86 Å2 / Biso mean: 23.83 Å2 / Biso min: 7.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.0348 Å20 Å20 Å2
2--0.6632 Å20 Å2
3----1.698 Å2
Refine analyzeLuzzati coordinate error obs: 0.163 Å
Refinement stepCycle: final / Resolution: 1.45→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4806 0 4 668 5478
Biso mean--47.63 33.82 -
Num. residues----595
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1814SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes732HARMONIC5
X-RAY DIFFRACTIONt_it5035HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion647SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6756SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5035HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6821HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion4.08
X-RAY DIFFRACTIONt_other_torsion17.14
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2421 387 4.91 %
Rwork0.2175 7490 -
all0.2187 7877 -
obs--99.99 %

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