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

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Basic information

Entry
Database: PDB / ID: 6bab
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


Phase 0 - rapid depolarisation / regulation of relaxation of cardiac muscle / HSF1-dependent transactivation / Interferon gamma signaling / Ion transport by P-type ATPases / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of AMPA receptors / RAF activation ...Phase 0 - rapid depolarisation / regulation of relaxation of cardiac muscle / HSF1-dependent transactivation / Interferon gamma signaling / Ion transport by P-type ATPases / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of AMPA receptors / RAF activation / protein serine/threonine kinase activity => GO:0004674 / regulation of cell communication by electrical coupling / cell growth involved in cardiac muscle cell development / calcium- and calmodulin-dependent protein kinase complex / RAF/MAP kinase cascade / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / axon initial segment / regulation of membrane depolarization / intracellular potassium ion homeostasis / Ion homeostasis / cardiac muscle cell contraction / endoplasmic reticulum calcium ion homeostasis / sodium channel inhibitor activity / relaxation of cardiac muscle / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / calcium/calmodulin-dependent protein kinase activity / regulation of cardiac muscle cell action potential / positive regulation of DNA biosynthetic process / nitric-oxide synthase binding / positive regulation of cardiac muscle hypertrophy / positive regulation of cardiac muscle cell apoptotic process / positive regulation of smooth muscle cell migration / positive regulation of Rac protein signal transduction / intercalated disc / regulation of protein localization to plasma membrane / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cardiac muscle contraction / regulation of sodium ion transport / titin binding / positive regulation of vascular associated smooth muscle cell proliferation / T-tubule / sarcoplasmic reticulum membrane / positive regulation of G2/M transition of mitotic cell cycle / sarcoplasmic reticulum / peptidyl-threonine phosphorylation / neuromuscular junction / G1/S transition of mitotic cell cycle / calcium ion transport / peptidyl-serine phosphorylation / transmembrane transporter binding / protein autophosphorylation / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / response to hypoxia / protein kinase activity / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / perinuclear region of cytoplasm / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
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-D0S / L(+)-TARTARIC ACID / Calcium/calmodulin-dependent protein kinase type II subunit delta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsSomoza, J.R. / Villasenor, A.G.
CitationJournal: To Be Published
Title: TBD
Authors: Koltun, D. / Somoza, J.R.
History
DepositionOct 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release

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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
C: Calcium/calmodulin-dependent protein kinase type II subunit delta
D: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,31111
Polymers137,8384
Non-polymers2,4737
Water16,862936
1
A: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1153
Polymers34,4601
Non-polymers6562
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)35,1153
Polymers34,4601
Non-polymers6562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1153
Polymers34,4601
Non-polymers6562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9652
Polymers34,4601
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.250, 67.570, 82.840
Angle α, β, γ (deg.)93.34, 92.93, 90.11
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Camk2d, Kiaa4163 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6PHZ2, Ca2+/calmodulin-dependent protein kinase
#2: Chemical
ChemComp-D0S / N-[(2S)-2-(diethylamino)propyl]-2-(3-hydroxyazetidin-1-yl)-6-[5-(thiophen-2-yl)pyrazolo[1,5-a]pyrimidin-3-yl]pyridine-4-carboxamide


Mass: 505.635 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H31N7O2S
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 936 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.91→54.2 Å / Num. obs: 80037 / % possible obs: 87.4 % / Redundancy: 2 % / Biso Wilson estimate: 22.25 Å2 / Net I/σ(I): 7.6

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→54.18 Å / SU ML: 0.248 / Cross valid method: FREE R-VALUE / σ(F): 1.986 / Phase error: 27.233
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.253 1330 1.685 %
Rwork0.19 --
obs0.191 78940 86.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.33 Å2
Refinement stepCycle: LAST / Resolution: 1.91→54.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9240 0 174 936 10350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069675
X-RAY DIFFRACTIONf_angle_d0.82513101
X-RAY DIFFRACTIONf_dihedral_angle_d16.9655762
X-RAY DIFFRACTIONf_chiral_restr0.051392
X-RAY DIFFRACTIONf_plane_restr0.0061676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.97830.31671390.23067821X-RAY DIFFRACTION87
1.9783-2.05750.30611140.21487642X-RAY DIFFRACTION85
2.0575-2.15110.26931220.20686863X-RAY DIFFRACTION77
2.1511-2.26450.29351360.20867631X-RAY DIFFRACTION85
2.2645-2.40640.25231380.19878136X-RAY DIFFRACTION91
2.4064-2.59220.27751410.20458148X-RAY DIFFRACTION91
2.5922-2.85310.26881330.20378061X-RAY DIFFRACTION90
2.8531-3.26590.28081370.19357773X-RAY DIFFRACTION87
3.2659-4.11440.22581190.16717073X-RAY DIFFRACTION79
4.1144-54.20020.20761510.17228462X-RAY DIFFRACTION95

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