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- PDB-6ayw: The structure of human CamKII with bound inhibitor -

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Basic information

Entry
Database: PDB / ID: 6ayw
TitleThe structure of human CamKII with bound inhibitor
ComponentsCalcium/calmodulin-dependent protein kinase type II subunit delta
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / Kinase / CamKII / inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / calcium- and calmodulin-dependent protein kinase complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / regulation of the force of heart contraction / Trafficking of AMPA receptors ...regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / calcium- and calmodulin-dependent protein kinase complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / regulation of the force of heart contraction / Trafficking of AMPA receptors / cardiac muscle cell contraction / endoplasmic reticulum calcium ion homeostasis / Assembly and cell surface presentation of NMDA receptors / sodium channel inhibitor activity / calmodulin-dependent protein kinase activity / regulation of heart contraction / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / relaxation of cardiac muscle / CaMK IV-mediated phosphorylation of CREB / regulation of cardiac muscle cell action potential / regulation of membrane depolarization / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of cardiac muscle hypertrophy / positive regulation of cardiac muscle cell apoptotic process / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / Long-term potentiation / Ion transport by P-type ATPases / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / sarcoplasmic reticulum membrane / cellular response to calcium ion / Ras activation upon Ca2+ influx through NMDA receptor / regulation of cell growth / peptidyl-threonine phosphorylation / RAF activation / sarcolemma / 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 / Interferon gamma signaling / Signaling by BRAF and RAF1 fusions / RAF/MAP kinase cascade / peptidyl-serine phosphorylation / transmembrane transporter binding / protein autophosphorylation / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-C2V / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Calcium/calmodulin-dependent protein kinase type II subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSomoza, J.R. / Villasenor, A.G.
CitationJournal: To Be Published
Title: The structure of human CamKII with bound inhibitor
Authors: Somoza, J.R. / Villasenor, A.G.
History
DepositionSep 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 delta
B: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0116
Polymers68,9192
Non-polymers1,0914
Water4,666259
1
A: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0053
Polymers34,4601
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0053
Polymers34,4601
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.149, 68.110, 84.825
Angle α, β, γ (deg.)90.000, 94.558, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 34459.574 Da / Num. of mol.: 2 / Fragment: UNP residues 3-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2D, CAMKD / Production host: unidentified baculovirus
References: UniProt: Q13557, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-C2V / N-[2-(dimethylamino)ethyl]-3-[6-(thiophen-2-yl)imidazo[1,2-b]pyridazin-3-yl]benzamide


Mass: 391.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21N5OS
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 microL ...Details: CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 microL aliquots. The protein was thawed and diluted down to 12 mg/mL in the same buffer just prior to crystallization experiments. Sitting drop vapor diffusion droplets were assembled with 250 nL of 12 mg/mL CamKII, 0.6 mM inhibitor and 250 nL of reservoir solution 24% peg 3350, 0.2 M ammonium tartrate, 0.1 M arginine. Flat crystal plates (typically 0.03 mm x 0.2 mm x 0.4 mm in size) grew in 4-7 days at 20 C. A crystal seed suspension was prepared with ten crushed crystals combined into 100 uL of reservoir solution and stored at -80 C. A thirty fold seed dilution was prepared in the same solution for addition to protein droplets in a 1 to 1 volume ratio to enhance crystallization of difficult to crystallize inhibitors.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 36488 / % possible obs: 94.9 % / Redundancy: 2.8 % / Net I/σ(I): 18.7

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Processing

Software
NameVersionClassification
HKL-2000data processing
EPMRphasing
PHENIX(phenix.refine: 1.12_2829)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→47.23 Å / SU ML: 0.271 / Cross valid method: FREE R-VALUE / σ(F): 1.337 / Phase error: 31.91
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2669 2008 5.52 %
Rwork0.1985 34318 -
obs0.202 36326 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.2 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4712 0 72 259 5043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074902
X-RAY DIFFRACTIONf_angle_d0.8686629
X-RAY DIFFRACTIONf_chiral_restr0.051707
X-RAY DIFFRACTIONf_plane_restr0.006850
X-RAY DIFFRACTIONf_dihedral_angle_d12.312947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.39171060.28741687X-RAY DIFFRACTION65.17
2.1-2.160.35131390.25722255X-RAY DIFFRACTION86.99
2.16-2.220.28831390.24582463X-RAY DIFFRACTION94.2
2.22-2.290.30851410.24082546X-RAY DIFFRACTION98.06
2.29-2.380.32951550.22632574X-RAY DIFFRACTION98.87
2.38-2.470.29171500.23162579X-RAY DIFFRACTION99.05
2.47-2.580.33121540.22722576X-RAY DIFFRACTION99.09
2.58-2.720.28961470.22572595X-RAY DIFFRACTION98.77
2.72-2.890.28151560.22262556X-RAY DIFFRACTION99.12
2.89-3.110.30981470.2172598X-RAY DIFFRACTION98.42
3.11-3.430.25761500.20572515X-RAY DIFFRACTION96.98
3.43-3.920.23481390.17882482X-RAY DIFFRACTION94.55
3.92-4.940.22231460.15462425X-RAY DIFFRACTION91.59
4.94-47.240.22421390.16692467X-RAY DIFFRACTION91.63

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