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- PDB-7ujr: Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain a... -

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Basic information

Entry
Database: PDB / ID: 7ujr
TitleCocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B
Components
  • Calcium/calmodulin-dependent protein kinase type II subunit alpha
  • Glutamate receptor ionotropic, NMDA 2B
KeywordsTRANSFERASE / CaMKII / Kinase / Human / CAMK2A
Function / homology
Function and homology information


peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / excitatory chemical synaptic transmission / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / Synaptic adhesion-like molecules / Activated NTRK2 signals through FYN / dendritic spine development ...peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / excitatory chemical synaptic transmission / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / Synaptic adhesion-like molecules / Activated NTRK2 signals through FYN / dendritic spine development / Trafficking of AMPA receptors / positive regulation of calcium ion transport / positive regulation of cysteine-type endopeptidase activity / glutamate-gated calcium ion channel activity / negative regulation of hydrolase activity / glutamate receptor signaling pathway / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / negative regulation of dendritic spine maintenance / Neurexins and neuroligins / calmodulin-dependent protein kinase activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / protein heterotetramerization / regulation of mitochondrial membrane permeability involved in apoptotic process / glutamate binding / glycine binding / CaMK IV-mediated phosphorylation of CREB / regulation of neuronal synaptic plasticity / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of cardiac muscle cell apoptotic process / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / monoatomic cation transmembrane transport / positive regulation of excitatory postsynaptic potential / Long-term potentiation / Ion transport by P-type ATPases / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / glutamate receptor binding / cellular response to interferon-beta / MECP2 regulates neuronal receptors and channels / Ion homeostasis / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / EPHB-mediated forward signaling / excitatory postsynaptic potential / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / response to ischemia / angiotensin-activated signaling pathway / postsynaptic density membrane / brain development / regulation of synaptic plasticity / G1/S transition of mitotic cell cycle / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / cellular response to type II interferon / endocytic vesicle membrane / 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 / calcium ion transport / Interferon gamma signaling / Signaling by BRAF and RAF1 fusions / late endosome / Ca2+ pathway / amyloid-beta binding / positive regulation of NF-kappaB transcription factor activity / kinase activity / chemical synaptic transmission / RAF/MAP kinase cascade / postsynaptic membrane / peptidyl-serine phosphorylation / response to ethanol / dendritic spine / postsynaptic density / protein autophosphorylation / lysosome / learning or memory / cytoskeleton / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / cell surface / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / ATP binding / identical protein binding
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / NTF2-like domain superfamily / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / NTF2-like domain superfamily / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / 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
Glutamate receptor ionotropic, NMDA 2B / Calcium/calmodulin-dependent protein kinase type II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsOzden, C. / Santos, N.J. / Stratton, M.M. / Garman, S.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2022
Title: CaMKII binds both substrates and activators at the active site.
Authors: Ozden, C. / Sloutsky, R. / Mitsugi, T. / Santos, N. / Agnello, E. / Gaubitz, C. / Foster, J. / Lapinskas, E. / Esposito, E.A. / Saneyoshi, T. / Kelch, B.A. / Garman, S.C. / Hayashi, Y. / Stratton, M.M.
History
DepositionMar 31, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionApr 13, 2022ID: 6XDL
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5856
Polymers33,3032
Non-polymers2824
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-5 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.090, 66.005, 45.002
Angle α, β, γ (deg.)90.000, 97.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calcium/calmodulin-dependent protein kinase type II subunit alpha / / CaMK-II subunit alpha


Mass: 30549.074 Da / Num. of mol.: 1 / Mutation: Q223K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2A, CAMKA, KIAA0968 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase
#2: Protein/peptide Glutamate receptor ionotropic, NMDA 2B / GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / ...GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / NR2B / N-methyl-D-aspartate receptor subunit 3 / hNR3


Mass: 2754.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13224
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.1 M Ammonium sulfate, 20% PEG 3350, 5% Ethanol

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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: Nov 18, 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: 1.95→50 Å / Num. obs: 17848 / % possible obs: 93.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.094 / Rrim(I) all: 0.161 / Χ2: 5.482 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.96-1.992.50.4857570.7580.3460.5991.63982.7
1.99-2.032.80.4248350.7980.2950.5191.55588.5
2.03-2.072.70.3238580.8610.2270.3961.6888.5
2.07-2.112.80.3198450.8780.220.391.88391.2
2.11-2.162.70.2648780.9060.1850.3241.95990.7
2.16-2.212.80.248540.9230.1680.2941.99891.8
2.21-2.262.80.2248890.9170.1550.2742.27693.7
2.26-2.322.90.1988710.9320.1370.2412.23994.2
2.32-2.392.80.1799190.940.1260.222.26195.5
2.39-2.472.80.1899140.9280.1330.2322.69796.6
2.47-2.562.80.39150.1440.2360.3835.97296.7
2.56-2.662.80.1549310.9530.1090.193.54496.1
2.66-2.782.80.1439220.960.0990.1754.01297.6
2.78-2.932.70.148880.960.0980.1725.00196.6
2.93-3.112.70.1389300.9520.0970.176.7495.9
3.11-3.352.70.1249070.9590.0860.1528.54295.4
3.35-3.692.70.1199270.9630.0830.14612.85395.5
3.69-4.222.60.1059200.9660.0760.1313.89496.5
4.22-5.322.60.1069290.9570.0790.13215.07396.1
5.32-502.40.1089590.9570.0830.13714.82196.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6vzk

6vzk


Resolution: 1.95→33.92 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.667 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 903 5.1 %RANDOM
Rwork0.2093 ---
obs0.2114 16929 93.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.72 Å2 / Biso mean: 28.074 Å2 / Biso min: 19.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å2-0.27 Å2
2--0.57 Å2-0 Å2
3----1.23 Å2
Refinement stepCycle: final / Resolution: 1.95→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 17 93 2344
Biso mean--45.15 33.63 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132304
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172130
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.6393122
X-RAY DIFFRACTIONr_angle_other_deg1.0941.5744917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8575279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.96121.721122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72915377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0011515
X-RAY DIFFRACTIONr_chiral_restr0.0450.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022561
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02500
LS refinement shellResolution: 1.951→2.002 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 55 -
Rwork0.272 1027 -
all-1082 -
obs--77.84 %

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