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- PDB-6x5q: Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain a... -

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Basic information

Entry
Database: PDB / ID: 6x5q
TitleCocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluA1
Components
  • Calcium/calmodulin-dependent protein kinase type II subunit alpha
  • Glutamate receptor 1
KeywordsTRANSFERASE / CaMKII / Kinase / Human / CAMK2A
Function / homology
Function and homology information


Activation of AMPA receptors / peptidyl-threonine autophosphorylation / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / axonal spine / Trafficking of GluR2-containing AMPA receptors / positive regulation of membrane potential / Ca2+/calmodulin-dependent protein kinase / cellular response to ammonium ion ...Activation of AMPA receptors / peptidyl-threonine autophosphorylation / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / axonal spine / Trafficking of GluR2-containing AMPA receptors / positive regulation of membrane potential / Ca2+/calmodulin-dependent protein kinase / cellular response to ammonium ion / dendritic spine development / negative regulation of hydrolase activity / regulation of neurotransmitter secretion / neuron spine / myosin V binding / Synaptic adhesion-like molecules / Trafficking of AMPA receptors / Cargo concentration in the ER / response to arsenic-containing substance / positive regulation of calcium ion transport / regulation of neuron migration / calcium/calmodulin-dependent protein kinase activity / cellular response to dsRNA / glutamate receptor activity / dendritic spine membrane / long-term synaptic depression / Assembly and cell surface presentation of NMDA receptors / regulation of mitochondrial membrane permeability involved in apoptotic process / beta-2 adrenergic receptor binding / COPII-mediated vesicle transport / cellular response to peptide hormone stimulus / neuronal cell body membrane / CaMK IV-mediated phosphorylation of CREB / cellular response to amine stimulus / protein kinase A binding / spinal cord development / perisynaptic space / Phase 0 - rapid depolarisation / AMPA glutamate receptor activity / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / response to lithium ion / Ion transport by P-type ATPases / AMPA glutamate receptor complex / adenylate cyclase binding / Long-term potentiation / immunoglobulin binding / Regulation of MECP2 expression and activity / excitatory synapse / response to electrical stimulus / regulation of receptor recycling / regulation of neuronal synaptic plasticity / G-protein alpha-subunit binding / glutamate receptor binding / HSF1-dependent transactivation / long-term memory / postsynaptic density, intracellular component / positive regulation of cardiac muscle cell apoptotic process / neuronal action potential / regulation of protein localization to plasma membrane / cellular response to interferon-beta / response to fungicide / synapse assembly / Ion homeostasis / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / dendritic shaft / response to ischemia / angiotensin-activated signaling pathway / response to cocaine / positive regulation of receptor signaling pathway via JAK-STAT / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / cellular response to amino acid stimulus / neuromuscular junction / ER to Golgi transport vesicle membrane / RAF activation / G1/S transition of mitotic cell cycle / : / postsynaptic density membrane / recycling endosome / cerebral cortex development / modulation of chemical synaptic transmission / cellular response to type II interferon / receptor internalization / small GTPase binding / long-term synaptic potentiation / recycling endosome membrane / 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
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / 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 ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / 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 1 / Calcium/calmodulin-dependent protein kinase type II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 Å
AuthorsOzden, C. / Stratton, M.M. / Garman, S.C.
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
DepositionMay 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1485
Polymers32,8722
Non-polymers2763
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-9 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.629, 57.456, 107.707
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(DE3) (bacteria)
References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase
#2: Protein/peptide Glutamate receptor 1 / GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ionotropic / ...GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ionotropic / AMPA 1 / GluA1


Mass: 2323.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42261
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris, 28% w/v PEG 4000

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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: Jan 29, 2020 / 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: 2.1→50 Å / Num. obs: 15265 / % possible obs: 96.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.091 / Rrim(I) all: 0.202 / Χ2: 0.746 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.14-2.184.40.3777240.8920.1940.4260.62892.7
2.18-2.224.60.3917130.8930.1990.4410.60394.6
2.22-2.264.70.3977330.880.2010.4470.64493.6
2.26-2.314.80.5077320.8090.2510.5671.1698.5
2.31-2.3650.5247470.0130.3890.6630.82295.3
2.36-2.415.10.3067480.9220.1470.3410.60996
2.41-2.4750.2917530.9440.140.3240.65598.8
2.47-2.545.20.2857460.9530.1350.3170.57694.2
2.54-2.615.20.2857570.950.1340.3160.58499.6
2.61-2.75.30.2727400.9540.1280.3020.65994.4
2.7-2.795.10.2787760.9610.1320.3090.7199.7
2.79-2.95.30.2087590.950.0990.2310.63896.1
2.9-3.045.10.1777630.9730.0840.1960.60198.6
3.04-3.25.10.1627570.9830.0770.180.72597.8
3.2-3.45.10.1347750.9840.0640.1490.73697.6
3.4-3.665.10.1297910.9870.0610.1431.02498.1
3.66-4.034.90.1267830.9850.0610.141.198.6
4.03-4.614.90.0937900.9920.0460.1040.89998.8
4.61-5.814.60.0988090.9850.050.1110.72698.2
5.81-504.10.0858690.9950.0450.0970.80897.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VZK

6vzk


Resolution: 2.14→39.32 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.892 / SU B: 5.435 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.235 754 5 %RANDOM
Rwork0.1893 ---
obs0.1915 14475 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.49 Å2 / Biso mean: 15.884 Å2 / Biso min: 1.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.94 Å2-0 Å2
3----0.88 Å2
Refinement stepCycle: final / Resolution: 2.14→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2241 0 18 96 2355
Biso mean--30.61 14.48 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132311
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172162
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.6363126
X-RAY DIFFRACTIONr_angle_other_deg1.291.5745006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7595282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20322.174115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55915388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7881513
X-RAY DIFFRACTIONr_chiral_restr0.070.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022550
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02481
LS refinement shellResolution: 2.104→2.159 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 36 -
Rwork0.224 798 -
all-834 -
obs--72.21 %

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