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- PDB-5uy6: Crystal Structure of the Human CAMKK2B -

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Basic information

Entry
Database: PDB / ID: 5uy6
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 / calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / 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 / calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / 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-8R4 / Calcium/calmodulin-dependent protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCounago, R.M. / Dewry, D. / Bountra, C. / 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. / Dewry, D. / Bountra, C. / Arruda, P. / Edwards, A.M. / Gileadi, O. / Structural Genomics Consortium (SGC)
History
DepositionFeb 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _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)33,5112
Polymers33,1271
Non-polymers3831
Water6,666370
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.324, 73.324, 121.964
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-8R4 / 2-cyclopentyl-4-(5-phenylfuro[2,3-b]pyridin-3-yl)benzoic acid


Mass: 383.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H21NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3350; 0.1M Bis-Tris; 0.2M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→19.75 Å / Num. obs: 37374 / % possible obs: 99.9 % / Redundancy: 21.7 % / Biso Wilson estimate: 26.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.032 / Net I/σ(I): 14.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 22.1 % / Rmerge(I) obs: 1.837 / Mean I/σ(I) obs: 2 / Num. unique obs: 1939 / CC1/2: 0.751 / Rpim(I) all: 0.398 / % 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: 1.7→19.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.095 / SU Rfree Blow DPI: 0.088 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1767 4.74 %RANDOM
Rwork0.16 ---
obs0.161 37306 100 %-
Displacement parametersBiso mean: 29.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.7656 Å20 Å20 Å2
2---0.7656 Å20 Å2
3---1.5312 Å2
Refinement stepCycle: 1 / Resolution: 1.7→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 29 370 2642
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014607HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.058380HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1075SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes644HARMONIC5
X-RAY DIFFRACTIONt_it4607HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.88
X-RAY DIFFRACTIONt_other_torsion13.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion295SEMIHARMONIC5
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_contact5063SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2252 119 4.18 %
Rwork0.196 2731 -
all0.1972 2850 -
obs--100 %
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)
13.16852.1193-0.67771.60320.24651.39760.0222-0.33850.04340.1277-0.22070.1144-0.0225-0.21580.1985-0.0407-0.00340.02950.0038-0.031-0.02074.025221.228755.272
21.24940.57130.30423.98041.95912.636-0.032-0.06030.06720.1304-0.11610.18080.0166-0.25890.1481-0.02470.01250.0098-0.03550.001-0.03525.39825.731254.8958
31.7397-0.9820.22753.1801-2.28021.2407-0.00560.1630.06-0.0029-0.004-0.0986-0.06470.11690.00960.1266-0.0146-0.0274-0.03590.01380.064519.606248.374666.4102
41.19-0.723-0.50421.89551.19463.11970.0319-0.00230.0778-0.1455-0.10670.1334-0.4597-0.27020.07480.02120.0368-0.0008-0.0570.0073-0.03217.865634.011947.6569
50.80870.04790.01940.67630.03860.7210.00450.0203-0.0302-0.0524-0.02460.006-0.05970.00150.02010.0131-0.00260.0085-0.05350.0073-0.034920.539425.738342.6337
60.6439-0.1810.0511.70980.15380.70160.01530.01450.06840.00870.0016-0.1341-0.14010.1156-0.01690.02-0.02430.0101-0.03770.011-0.014532.168533.396747.598
70.80590.1468-0.10611.0947-0.13582.1690.04850.00470.0233-0.034-0.0121-0.1956-0.02110.1786-0.0364-0.0715-0.0110.0264-0.06140.01-0.030138.42826.157742.9793
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 - 343}
6X-RAY DIFFRACTION6{A|344 - 385}
7X-RAY DIFFRACTION7{A|386 - 448}

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