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- PDB-6vzk: Crystal structure of human CaMKII-alpha (CAMK2A)kinase domain -

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Basic information

Entry
Database: PDB / ID: 6vzk
TitleCrystal structure of human CaMKII-alpha (CAMK2A)kinase domain
ComponentsCalcium/calmodulin-dependent protein kinase type II subunit alpha
KeywordsTRANSFERASE / CaMKII / Kinase / Human / CAMK2A
Function / homology
Function and homology information


peptidyl-threonine autophosphorylation / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / Ca2+/calmodulin-dependent protein kinase / negative regulation of hydrolase activity / dendritic spine development / regulation of neurotransmitter secretion / Trafficking of AMPA receptors / positive regulation of calcium ion transport / regulation of neuron migration ...peptidyl-threonine autophosphorylation / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / Ca2+/calmodulin-dependent protein kinase / negative regulation of hydrolase activity / dendritic spine development / regulation of neurotransmitter secretion / Trafficking of AMPA receptors / positive regulation of calcium ion transport / regulation of neuron migration / calcium/calmodulin-dependent protein kinase activity / regulation of mitochondrial membrane permeability involved in apoptotic process / Assembly and cell surface presentation of NMDA receptors / CaMK IV-mediated phosphorylation of CREB / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ferroptosis / Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / Long-term potentiation / HSF1-dependent transactivation / Regulation of MECP2 expression and activity / regulation of neuronal synaptic plasticity / glutamate receptor binding / regulation of protein localization to plasma membrane / cellular response to interferon-beta / Ion homeostasis / positive regulation of cardiac muscle cell apoptotic process / Ras activation upon Ca2+ influx through NMDA receptor / response to ischemia / angiotensin-activated signaling pathway / : / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / G1/S transition of mitotic cell cycle / cellular response to type II interferon / Interferon gamma signaling / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / kinase activity / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / calcium ion transport / long-term synaptic potentiation / RAF/MAP kinase cascade / Ca2+ pathway / dendritic spine / protein phosphorylation / calmodulin binding / neuron projection / postsynaptic density / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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 ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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 / Alpha Beta
Similarity search - Domain/homology
4'-HYDROXYCINNAMIC ACID / Calcium/calmodulin-dependent protein kinase type II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsOzden, C. / Stratton, M.M. / Garman, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM123157 United States
CitationJournal: Protein Sci. / Year: 2020
Title: Characterization of CaMKII alpha holoenzyme stability.
Authors: Torres-Ocampo, A.P. / Ozden, C. / Hommer, A. / Gardella, A. / Lapinskas, E. / Samkutty, A. / Esposito, E. / Garman, S.C. / Stratton, M.M.
History
DepositionFeb 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 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 type II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7122
Polymers30,5481
Non-polymers1641
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.147, 56.928, 97.461
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 Calcium/calmodulin-dependent protein kinase type II subunit alpha / CaMK-II subunit alpha


Mass: 30548.086 Da / Num. of mol.: 1 / Mutation: D135N, Q223K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2A, CAMKA, KIAA0968 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, 50 mM HEPES, 3-Aminobenzene-sulfonic acid, 5-Sulfosalicylic acid dihydrate, p-Coumaric acid, PIPES, Terephthalic acid, Vanillic acid

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K thorughout the collection / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Mar 9, 2019 / Details: Rigaku VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 8711 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.093 / Rrim(I) all: 0.215 / Χ2: 0.916 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.7-2.755.23790.8640.4890.621100
2.75-2.85.23810.8770.4120.7021000.8590.956
2.8-2.855.43860.850.4060.62799.50.8680.96
2.85-2.915.53620.8250.3710.6381000.7860.871
2.91-2.975.43770.9080.2810.7031000.6040.668
2.97-3.045.53780.9140.2650.7241000.5770.637
3.04-3.125.83710.930.2350.7741000.5260.577
3.12-3.25.73890.9480.150.7631000.3270.36
3.2-3.35.83700.9530.1460.8171000.3290.36
3.3-3.45.93880.9750.0980.7691000.2220.243
3.4-3.525.83820.9870.0760.761000.170.186
3.52-3.665.93640.980.0770.8281000.1740.191
3.66-3.835.83860.9910.0640.7881000.1430.157
3.83-4.035.83990.990.0611.0111000.1360.15
4.03-4.295.83740.990.0551.0421000.1230.135
4.29-4.625.73940.9920.0491.2361000.1080.119
4.62-5.085.63950.990.0520.8761000.1120.124
5.08-5.815.43950.980.0731.0531000.1570.174
5.81-7.325.24070.9820.0771.1821000.1630.181
7.32-504.34450.9670.0542.57398.20.1030.117

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SOA

3soa


Resolution: 2.55→43.2 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.868 / SU B: 14.04 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.348 / ESU R Free: 0.375
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2944 446 4.9 %RANDOM
Rwork0.2103 ---
obs0.2142 8711 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103 Å2 / Biso mean: 34.924 Å2 / Biso min: 16.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å2-0 Å2-0 Å2
2---2.43 Å20 Å2
3---1.52 Å2
Refinement stepCycle: final / Resolution: 2.55→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 12 5 2092
Biso mean--35.37 22.35 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132140
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171983
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.6442900
X-RAY DIFFRACTIONr_angle_other_deg1.1981.5784593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7055255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24222.241116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.4615358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2881513
X-RAY DIFFRACTIONr_chiral_restr0.070.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022380
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02463
LS refinement shellResolution: 2.552→2.618 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 32 -
Rwork0.288 603 -
all-635 -
obs--98.15 %

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