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- PDB-1hkx: Crystal structure of calcium/calmodulin-dependent protein kinase -

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Basic information

Entry
Database: PDB / ID: 1hkx
TitleCrystal structure of calcium/calmodulin-dependent protein kinase
ComponentsCALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / CALMODULIN-BINDING / PHOSPHORYLATION / ATP-BINDING / ALTERNATIVE SPLICING
Function / homology
Function and homology information


regulation of synaptic vesicle docking / HSF1-dependent transactivation / Interferon gamma signaling / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / regulation of endocannabinoid signaling pathway / RAF activation / calcium- and calmodulin-dependent protein kinase complex / Trafficking of AMPA receptors ...regulation of synaptic vesicle docking / HSF1-dependent transactivation / Interferon gamma signaling / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / regulation of endocannabinoid signaling pathway / RAF activation / calcium- and calmodulin-dependent protein kinase complex / Trafficking of AMPA receptors / Ca2+ pathway / RAF/MAP kinase cascade / Ca2+/calmodulin-dependent protein kinase / negative regulation of hydrolase activity / dendritic spine development / regulation of neuron migration / regulation of neurotransmitter secretion / Ion homeostasis / positive regulation of calcium ion transport / calcium/calmodulin-dependent protein kinase activity / regulation of mitochondrial membrane permeability involved in apoptotic process / dendrite morphogenesis / regulation of neuronal synaptic plasticity / glutamate receptor binding / cellular response to interferon-beta / positive regulation of cardiac muscle cell apoptotic process / response to ischemia / positive regulation of receptor signaling pathway via JAK-STAT / Schaffer collateral - CA1 synapse / G1/S transition of mitotic cell cycle / calcium ion transport / dendritic spine / calmodulin binding / postsynaptic density / protein serine kinase activity / protein serine/threonine kinase activity / synapse / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / HEXATANTALUM DODECABROMIDE / Calcium/calmodulin-dependent protein kinase type II subunit alpha
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsHoelz, A. / Nairn, A.C. / Kuriyan, J.
CitationJournal: Mol.Cell / Year: 2003
Title: Crystal Structure of a Tetradecameric Assembly of the Association Domain of Ca2+/Calmodulin-Dependent Kinase II
Authors: Hoelz, A. / Nairn, A.C. / Kuriyan, J.
History
DepositionMar 12, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
B: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
C: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
D: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
E: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
F: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
G: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
H: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
I: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
J: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
K: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
L: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
M: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
N: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,04330
Polymers236,34814
Non-polymers2,69516
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)147.946, 118.043, 157.820
Angle α, β, γ (deg.)90.00, 110.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN / CAM-KINASE II ALPHA CHAIN / CAM KINASE II ALPHA SUBUNIT / CAMK-II ALPHA SUBUNIT / CAMK2A


Mass: 16881.994 Da / Num. of mol.: 14 / Fragment: ASSOCIATION DOMAIN, RESIDUES 336-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11798, EC: 2.7.1.123
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br12Ta6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS KINASE MAY PLAY A ROLE IN NEUROTRANSMISSION. CATALYES ATP + PROTEIN = ADP + O-PHOSPHOPROTEIN. ...THIS KINASE MAY PLAY A ROLE IN NEUROTRANSMISSION. CATALYES ATP + PROTEIN = ADP + O-PHOSPHOPROTEIN. AUTOPHOSPHORYLATION OF THR-286 MAY ALLOW THE KINASE TO SWITCH FROM A CALMODULIN-DEPENDENT TO A CALMODULIN- INDEPENDENT STATE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 55 %
Crystal growpH: 4.8 / Details: pH 4.80
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 4.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
135 mg/mlprotein1drop
220-25 %MPD1reservoir
3200 mM1reservoirNaCl
42 %PEG4001reservoir
520 mMmagnesium acetate1reservoir
6100 mMsodium acetate1reservoirpH4.8

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.9187,0.9191,1.2543
SYNCHROTRONALS 8.2.121.2545, 1.0038,1.0090
Detector
IDDate
1Mar 15, 2002
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91871
20.91911
31.25431
41.25451
51.00381
61.0091
ReflectionResolution: 2.65→20 Å / Num. obs: 73701 / % possible obs: 97.6 % / Redundancy: 4 % / Biso Wilson estimate: 61.9 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.3
Reflection shellResolution: 2.65→2.71 Å / Redundancy: 4 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2 / % possible all: 78.2
Reflection
*PLUS
Highest resolution: 2.65 Å / Lowest resolution: 20 Å / Num. measured all: 977524 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 78.2 % / Rmerge(I) obs: 0.444

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
RAVEphasing
CCP4phasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.65→19.84 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 175595.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 6774 5 %RANDOM
Rwork0.246 ---
obs0.246 135629 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.0973 Å2 / ksol: 0.30536 e/Å3
Displacement parametersBiso mean: 61.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å2-5.2 Å2
2---5.76 Å20 Å2
3---7.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.65→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15588 0 40 62 15690
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.851.5
X-RAY DIFFRACTIONc_mcangle_it3.412
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 850 4.7 %
Rwork0.358 17306 -
obs--75.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TBR_XPLOR.PARWATER.TOP
X-RAY DIFFRACTION3ION.PARAMDTT.TOP
X-RAY DIFFRACTION4WATER.PARAMION.TOP
X-RAY DIFFRACTION5DTT.PARTBR_XPLOR.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 4.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0081
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07

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