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

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Basic information

Entry
Database: PDB / ID: 7ujq
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 / Ca2+/calmodulin-dependent protein kinase / excitatory chemical synaptic transmission / regulation of neurotransmitter secretion / regulation of neuron migration / negative regulation of hydrolase activity / dendritic spine development / Activated NTRK2 signals through FYN ...peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / excitatory chemical synaptic transmission / regulation of neurotransmitter secretion / regulation of neuron migration / negative regulation of hydrolase activity / dendritic spine development / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / Trafficking of AMPA receptors / positive regulation of calcium ion transport / 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 / Neurexins and neuroligins / NMDA selective glutamate receptor complex / glutamate receptor signaling pathway / calcium ion transmembrane import into cytosol / CaMK IV-mediated phosphorylation of CREB / glutamate binding / protein heterotetramerization / glycine binding / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / Long-term potentiation / Regulation of MECP2 expression and activity / positive regulation of excitatory postsynaptic potential / HSF1-dependent transactivation / glutamate receptor binding / cellular response to interferon-beta / regulation of protein localization to plasma membrane / Ion homeostasis / positive regulation of cardiac muscle cell apoptotic process / MECP2 regulates neuronal receptors and channels / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / EPHB-mediated forward signaling / 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 / excitatory postsynaptic potential / response to ischemia / angiotensin-activated signaling pathway / synaptic transmission, glutamatergic / positive regulation of receptor signaling pathway via JAK-STAT / long-term synaptic potentiation / RAF activation / synaptic membrane / postsynaptic density membrane / brain development / regulation of synaptic plasticity / cellular response to type II interferon / G1/S transition of mitotic cell cycle / calcium ion transport / 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 / Interferon gamma signaling / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / kinase activity / late endosome / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / Ca2+ pathway / peptidyl-serine phosphorylation / RAF/MAP kinase cascade / protein autophosphorylation / chemical synaptic transmission / response to ethanol / postsynaptic membrane / dendritic spine / learning or memory / lysosome / cytoskeleton / calmodulin binding / postsynaptic density / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / endoplasmic reticulum membrane / cell surface / signal transduction / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm
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
Chem-UZD / 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: 2.25 Å
AuthorsOzden, C. / Foster, J.C. / 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: 6XBP
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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Glutamate receptor ionotropic, NMDA 2B
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3677
Polymers66,6044
Non-polymers7633
Water2,324129
1
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6383
Polymers33,3022
Non-polymers3351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-4 kcal/mol
Surface area13580 Å2
MethodPISA
2
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7304
Polymers33,3022
Non-polymers4272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-4 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.245, 91.784, 91.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRARGARGAA7 - 2741 - 268
21THRTHRARGARGBB7 - 2741 - 268
12ARGARGASPASPCC1295 - 13057 - 17
22ARGARGASPASPDD1295 - 13057 - 17

NCS ensembles :
ID
1
2

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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.: 2 / 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: 2754.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13224
#3: Chemical ChemComp-UZD / methyl 6-O-(heptylcarbamoyl)-beta-L-altropyranoside


Mass: 335.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H29NO7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M Bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane, 0.1 M Ammonium sulfate, 25% PEG 3350, 19mM Methyl 6-O-(N-heptylcarbamoyl)-alpha-D-glucopyranoside

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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 22, 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: 2.25→50 Å / Num. obs: 29074 / % possible obs: 96.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.05 / Rrim(I) all: 0.127 / Χ2: 2.896 / Net I/σ(I): 9.3 / Num. measured all: 182419
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.295.70.37413540.9170.1650.411.53590.1
2.29-2.3360.33413320.9410.1430.3641.45792.9
2.33-2.385.90.30713960.950.1330.3361.5894.7
2.38-2.4260.29714100.9520.1270.3241.75495.1
2.42-2.486.10.26514140.9620.1130.2891.66295.7
2.48-2.536.20.25614130.9670.1090.2791.74695.9
2.53-2.66.30.23314180.960.0990.2531.99595.9
2.6-2.676.40.21214260.9760.0890.231.90796.2
2.67-2.756.50.19214210.9810.080.2082.1696.3
2.75-2.836.60.16914440.9850.070.1842.21896.7
2.83-2.946.60.15314720.9870.0640.1662.52598
2.94-3.056.60.19914550.9890.0870.2173.08398.1
3.05-3.196.60.11814620.990.0490.1283.00898.7
3.19-3.366.60.10514830.9920.0440.1143.0399.1
3.36-3.576.60.09314660.9930.0390.1013.74898.7
3.57-3.856.50.09215090.9930.0390.14.07999.1
3.85-4.236.40.08314970.9930.0360.093.98699.2
4.23-4.856.30.07915280.9940.0340.0874.46899.3
4.85-6.16.10.08615440.9930.0380.0944.49399.6
6.1-505.40.07716300.9920.0370.0866.70199

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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: 2.25→45.93 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.892 / SU B: 6.799 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 1376 4.7 %RANDOM
Rwork0.2199 ---
obs0.2223 27648 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.67 Å2 / Biso mean: 24.97 Å2 / Biso min: 9.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0 Å20 Å2
2---1.27 Å20 Å2
3---1.94 Å2
Refinement stepCycle: final / Resolution: 2.25→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4507 0 52 129 4688
Biso mean--23.01 21.49 -
Num. residues----562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0134671
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174352
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.6526321
X-RAY DIFFRACTIONr_angle_other_deg1.0881.59410083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79621.928249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80415786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7351531
X-RAY DIFFRACTIONr_chiral_restr0.0490.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025152
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02996
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A83340.1
12B83340.1
21C2050.15
22D2050.15
LS refinement shellResolution: 2.252→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 93 -
Rwork0.254 1847 -
all-1940 -
obs--89.61 %

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