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- PDB-7kl2: Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain a... -

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Entry
Database: PDB / ID: 7kl2
TitleCocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D)
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 / Ca2+/calmodulin-dependent protein kinase / excitatory chemical synaptic transmission / negative regulation of hydrolase activity / dendritic spine development / Activated NTRK2 signals through FYN / regulation of neurotransmitter secretion / Synaptic adhesion-like molecules ...peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / excitatory chemical synaptic transmission / negative regulation of hydrolase activity / dendritic spine development / Activated NTRK2 signals through FYN / regulation of neurotransmitter secretion / Synaptic adhesion-like molecules / Trafficking of AMPA receptors / positive regulation of calcium ion transport / regulation of neuron migration / negative regulation of dendritic spine maintenance / calcium/calmodulin-dependent protein kinase activity / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / regulation of mitochondrial membrane permeability involved in apoptotic process / NMDA selective glutamate receptor complex / Neurexins and neuroligins / glutamate binding / glutamate receptor signaling pathway / CaMK IV-mediated phosphorylation of CREB / calcium ion transmembrane import into cytosol / protein heterotetramerization / glycine binding / Phase 0 - rapid depolarisation / monoatomic cation transmembrane transport / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / Long-term potentiation / Regulation of MECP2 expression and activity / positive regulation of excitatory postsynaptic potential / regulation of neuronal synaptic plasticity / HSF1-dependent transactivation / glutamate receptor binding / regulation of protein localization to plasma membrane / cellular response to interferon-beta / positive regulation of cardiac muscle cell apoptotic process / MECP2 regulates neuronal receptors and channels / Ion homeostasis / glutamate-gated calcium ion channel activity / EPHB-mediated forward signaling / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of synaptic transmission, glutamatergic / response to ischemia / excitatory postsynaptic potential / angiotensin-activated signaling pathway / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / positive regulation of receptor signaling pathway via JAK-STAT / synaptic membrane / RAF activation / G1/S transition of mitotic cell cycle / postsynaptic density membrane / positive regulation of NF-kappaB transcription factor activity / brain development / regulation of synaptic plasticity / cellular response to type II interferon / long-term synaptic potentiation / 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 / calcium ion transport / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / kinase activity / late endosome / amyloid-beta binding / Ca2+ pathway / RAF/MAP kinase cascade / response to ethanol / chemical synaptic transmission / dendritic spine / postsynaptic membrane / learning or memory / cytoskeleton / lysosome / calmodulin binding / neuron projection / postsynaptic density / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / endoplasmic reticulum membrane / cell surface / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / ATP binding / metal ion 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 / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel ...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 / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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: 2.56 Å
AuthorsOzden, C. / Stratton, M.M. / Garman, S.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D)
Authors: Ozden, C. / Stratton, M.M. / Garman, S.C.
History
DepositionOct 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 2.0Apr 6, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_mon_prot_cis / struct_sheet_range
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.organism_common_name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id
Description: Atoms with unrealistic or zero occupancies
Details: We have gotten rid of some water and ligand molecules.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 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


Theoretical massNumber of molelcules
Total (without water)33,3302
Polymers33,3302
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-4 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.777, 65.162, 54.105
Angle α, β, γ (deg.)90.000, 95.800, 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: 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(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: 2782.165 Da / Num. of mol.: 1 / Mutation: S1303D / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13224
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.15 M DL-Malic acid pH 7, 20% PEG 3350

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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: Jul 8, 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: 9973 / % possible obs: 99.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.138 / Rrim(I) all: 0.238 / Χ2: 1.648 / Net I/σ(I): 3.2 / Num. measured all: 30971
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Χ2% possible allRpim(I) allRmerge(I) obsRrim(I) all
2.55-2.592.64710.1331.25297.7
2.59-2.642.85000.0481.37198.8
2.64-2.692.84840.1821.34699.2
2.69-2.752.94960.2951.28399.8
2.75-2.812.85160.2611.28499.2
2.81-2.8734640.3871.299100
2.87-2.942.95040.4721.29799.6
2.94-3.0235080.5981.3799.80.83
3.02-3.113.24930.631.3831000.5150.7760.936
3.11-3.213.25040.6451.6071000.3470.5280.635
3.21-3.333.35000.7951.5531000.2550.3920.47
3.33-3.463.44910.8561.59199.60.180.2810.335
3.46-3.623.45060.9041.78599.60.1680.2630.313
3.62-3.813.45040.9461.7291000.1240.1940.231
3.81-4.053.35060.9561.9081000.1310.2010.241
4.05-4.363.34890.971.85899.80.10.1530.183
4.36-4.83.35040.9712.0611000.0910.140.168
4.8-5.493.35110.9731.74499.40.0970.150.179
5.49-6.923.24990.9562.191000.1110.1690.203
6.92-502.95230.9892.64797.90.0580.0830.101

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VZK

6vzk


Resolution: 2.56→41.53 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.874 / SU B: 30.727 / SU ML: 0.546 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.383 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.293 500 5 %RANDOM
Rwork0.2439 ---
obs0.2466 9458 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.5 Å2 / Biso mean: 45.386 Å2 / Biso min: 16.38 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å2-0 Å20.88 Å2
2---0.85 Å2-0 Å2
3---2.64 Å2
Refinement stepCycle: final / Resolution: 2.56→41.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 0 6 2245
Biso mean---24.37 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132296
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172089
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.6373123
X-RAY DIFFRACTIONr_angle_other_deg1.141.5724816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4555282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02921.855124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.39115359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.831515
X-RAY DIFFRACTIONr_chiral_restr0.0560.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02503
LS refinement shellResolution: 2.56→2.623 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.373 32 -
Rwork0.417 577 -
obs--82.3 %

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