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- PDB-5uyj: Crystal Structure of the Human CAMKK2B -

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Basic information

Entry
Database: PDB / ID: 5uyj
TitleCrystal Structure of the Human CAMKK2B
ComponentsCalcium/calmodulin-dependent protein kinase kinase 2
KeywordsTransferase/Transferase Inhibitor / transferase / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor Complex
Function / homology
Function and homology information


positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / regulation of protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / calcium/calmodulin-dependent protein kinase activity / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / Activation of AMPK downstream of NMDARs / calcium-mediated signaling ...positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / regulation of protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / calcium/calmodulin-dependent protein kinase activity / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / Activation of AMPK downstream of NMDARs / calcium-mediated signaling / cellular response to reactive oxygen species / MAPK cascade / protein tyrosine kinase activity / protein autophosphorylation / calmodulin binding / neuron projection / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / cytosol
Similarity search - Function
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
Chem-8R7 / Calcium/calmodulin-dependent protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCounago, R.M. / Drewry, D. / Arruda, P. / Edwards, A.M. / Gileadi, O. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of the Human CAMKK2B
Authors: Counago, R.M. / Drewry, D. / Arruda, P. / Edwards, A.M. / Gileadi, O. / Structural Genomics Consortium (SGC)
History
DepositionFeb 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium/calmodulin-dependent protein kinase kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4752
Polymers33,1271
Non-polymers3471
Water6,089338
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.153, 73.153, 120.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Calcium/calmodulin-dependent protein kinase kinase 2 / CaMKK 2 / Calcium/calmodulin-dependent protein kinase kinase beta / CaMKK beta


Mass: 33127.250 Da / Num. of mol.: 1 / Fragment: UNP residues 161-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMKK2, CAMKKB, KIAA0787 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3
References: UniProt: Q96RR4, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-8R7 / 2-cyclopentyl-4-(7-methoxyquinolin-4-yl)benzoic acid


Mass: 347.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 20 mM Ammonium Sulphate, 0.1M Citric acid-Hepes-CHES buffer system

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.6→19.61 Å / Num. obs: 43864 / % possible obs: 99.9 % / Redundancy: 25.8 % / Biso Wilson estimate: 20.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.025 / Net I/av σ(I): 21.3 / Net I/σ(I): 21.3
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 10.9 / Num. unique obs: 2137 / CC1/2: 0.989 / Rpim(I) all: 0.063 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZV2

2zv2


Resolution: 1.6→19.61 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.074 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.066
RfactorNum. reflection% reflectionSelection details
Rfree0.171 2169 4.95 %RANDOM
Rwork0.153 ---
obs0.154 43790 100 %-
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.3455 Å20 Å20 Å2
2---0.3455 Å20 Å2
3---0.6911 Å2
Refinement stepCycle: 1 / Resolution: 1.6→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 26 338 2587
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014554HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.048282HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1320SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes645HARMONIC5
X-RAY DIFFRACTIONt_it4554HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.09
X-RAY DIFFRACTIONt_other_torsion2.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion296SEMIHARMONIC5
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_contact5135SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1627 154 4.87 %
Rwork0.1345 3007 -
all0.1358 3161 -
obs--99.97 %
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)
12.8040.7876-0.64651.363-0.21051.2780.0303-0.18580.04620.1065-0.05250.0794-0.0928-0.07970.0222-0.01160.00430.0197-0.0169-0.0035-0.0372-32.7182-15.6207-5.8819
22.55590.5571.40614.0071.25792.161-0.09-0.14530.09670.15710.00230.0712-0.0781-0.25690.0877-0.02230.01670.0234-0.02950.0001-0.0655-31.377-11.4458-6.5462
30.4121-1.6931.50582.3949-2.03572.1975-0.00450.08910.0109-0.0787-0.0114-0.0566-0.01810.04680.01590.13340.0195-0.03480.02050.0140.1126-17.547410.70344.4658
41.0971-0.4565-0.1861.62480.26782.2862-0.015-0.01150.1502-0.0132-0.00720.1322-0.3791-0.23790.02220.00450.02890.009-0.05870.0056-0.0269-28.5701-2.4715-13.4747
50.98790.0585-0.21960.7301-0.09230.6617-0.0322-0.0178-0.0811-0.02150.0003-0.03410.0549-0.01440.03190.0089-0.00240.002-0.04990.011-0.0335-15.9888-14.9415-19.0495
60.91590.6754-0.30540.849-0.37231.9102-0.0522-0.0048-0.0559-0.0573-0.0381-0.06650.0479-0.03190.0903-0.0117-0.00330.0167-0.03040.005-0.0117-16.5268-9.5907-17.6712
71.02851.2743-0.09952.4084-0.38560.5397-0.01090.00520.1226-0.0533-0.02170.1272-0.0311-0.04620.03250.01840.00890.0035-0.04370.0051-0.0137-16.9396-0.6192-17.396
80.4497-0.22540.04641.88260.31691.0328-0.0192-0.00380.02270.01050.0434-0.1257-0.04160.0677-0.0242-0.01850.00080.0079-0.02530.01850.0041-4.5617-3.3042-13.2794
90.50910.16480.04661.21840.03742.17010.03270.01620.0061-0.04410.0564-0.20330.10390.162-0.089-0.0920.01590.0235-0.06350.0113-0.02351.6095-10.498-18.036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|159 - 177}
2X-RAY DIFFRACTION2{A|178 - 205}
3X-RAY DIFFRACTION3{A|206 - 228}
4X-RAY DIFFRACTION4{A|229 - 261}
5X-RAY DIFFRACTION5{A|262 - 305}
6X-RAY DIFFRACTION6{A|306 - 325}
7X-RAY DIFFRACTION7{A|326 - 343}
8X-RAY DIFFRACTION8{A|344 - 385}
9X-RAY DIFFRACTION9{A|386 - 448}

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