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- PDB-4u40: Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) ... -

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Basic information

Entry
Database: PDB / ID: 4u40
TitleMitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) Bound to AMPPNP
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase kinase kinase kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 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)76,3196
Polymers75,7402
Non-polymers5794
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-48 kcal/mol
Surface area26540 Å2
MethodPISA
2
A: Mitogen-activated protein kinase kinase kinase kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4495
Polymers37,8701
Non-polymers5794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: 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
Unit cell
Length a, b, c (Å)80.339, 87.595, 91.450
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
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: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 31, 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: 2.3→50 Å / Num. obs: 29367 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 45.06 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.067 / Net I/av σ(I): 23.019 / Net I/σ(I): 9.6 / Num. measured all: 179281
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.386.20.58628841.022100
2.38-2.486.20.43428681.061100
2.48-2.596.20.33529241.069100
2.59-2.736.20.23928711.085100
2.73-2.96.20.18129211.099100
2.9-3.126.20.12329191.096100
3.12-3.446.20.08129131.079100
3.44-3.936.10.06329541.076100
3.93-4.9560.05229831.077100
4.95-505.70.04631301.00499.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.6.4_486)refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→40.169 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2615 1489 5.08 %
Rwork0.1983 27819 -
obs0.2014 29308 99.9 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.82 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso max: 128.13 Å2 / Biso mean: 56.5528 Å2 / Biso min: 27.37 Å2
Baniso -1Baniso -2Baniso -3
1--3.8066 Å20 Å2-0 Å2
2--10.3237 Å20 Å2
3----6.5171 Å2
Refinement stepCycle: final / Resolution: 2.3→40.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 34 155 4985
Biso mean--50.95 52.09 -
Num. residues----594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084950
X-RAY DIFFRACTIONf_angle_d1.1366702
X-RAY DIFFRACTIONf_chiral_restr0.083725
X-RAY DIFFRACTIONf_plane_restr0.004861
X-RAY DIFFRACTIONf_dihedral_angle_d16.2311876
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.37330.29841250.25412476260199
2.3733-2.45810.33681440.243724532597100
2.4581-2.55650.33821590.245324692628100
2.5565-2.67290.27761460.222525012647100
2.6729-2.81380.31881410.225624972638100
2.8138-2.990.27441220.224425272649100
2.99-3.22080.28211280.217625262654100
3.2208-3.54470.25821170.195425392656100
3.5447-4.05720.26551340.172625552689100
4.0572-5.110.22671470.169625722719100
5.11-40.17560.23141260.196727042830100

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