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- PDB-7urz: Hexadecameric hub domain of CaMKII beta -

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Basic information

Entry
Database: PDB / ID: 7urz
TitleHexadecameric hub domain of CaMKII beta
ComponentsCalcium/calmodulin-dependent protein kinase type II subunit beta
KeywordsTRANSFERASE / CaMKII / Kinase / Human / CAMK2B
Function / homology
Function and homology information


regulation of skeletal muscle adaptation / regulation of synapse structural plasticity / calcium- and calmodulin-dependent protein kinase complex / calcium-dependent protein serine/threonine kinase activity / regulation of dendritic spine development / positive regulation of synapse maturation / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / positive regulation of dendritic spine morphogenesis / Trafficking of AMPA receptors ...regulation of skeletal muscle adaptation / regulation of synapse structural plasticity / calcium- and calmodulin-dependent protein kinase complex / calcium-dependent protein serine/threonine kinase activity / regulation of dendritic spine development / positive regulation of synapse maturation / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / positive regulation of dendritic spine morphogenesis / Trafficking of AMPA receptors / Assembly and cell surface presentation of NMDA receptors / calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / regulation of calcium ion transport / Long-term potentiation / Ion transport by P-type ATPases / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / Ion homeostasis / sarcoplasmic reticulum membrane / Ras activation upon Ca2+ influx through NMDA receptor / regulation of long-term neuronal synaptic plasticity / RAF activation / positive regulation of neuron projection development / 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 / nervous system development / actin binding / RAF/MAP kinase cascade / peptidyl-serine phosphorylation / protein autophosphorylation / cell differentiation / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / centrosome / synapse / signal transduction / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / 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 / 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. ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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
Calcium/calmodulin-dependent protein kinase type II subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.45 Å
AuthorsOzden, C. / Samkutty, A. / Stratton, M.M. / Garman, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01123157 United States
CitationJournal: To Be Published
Title: Hexadecameric hub domain of CaMKII beta
Authors: Ozden, C. / Samkutty, A. / Stratton, M.M. / Garman, S.C.
History
DepositionApr 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
G: Calcium/calmodulin-dependent protein kinase type II subunit beta
A: Calcium/calmodulin-dependent protein kinase type II subunit beta
B: Calcium/calmodulin-dependent protein kinase type II subunit beta
C: Calcium/calmodulin-dependent protein kinase type II subunit beta


Theoretical massNumber of molelcules
Total (without water)62,3544
Polymers62,3544
Non-polymers00
Water0
1
G: Calcium/calmodulin-dependent protein kinase type II subunit beta
A: Calcium/calmodulin-dependent protein kinase type II subunit beta
B: Calcium/calmodulin-dependent protein kinase type II subunit beta
C: Calcium/calmodulin-dependent protein kinase type II subunit beta

G: Calcium/calmodulin-dependent protein kinase type II subunit beta
A: Calcium/calmodulin-dependent protein kinase type II subunit beta
B: Calcium/calmodulin-dependent protein kinase type II subunit beta
C: Calcium/calmodulin-dependent protein kinase type II subunit beta

G: Calcium/calmodulin-dependent protein kinase type II subunit beta
A: Calcium/calmodulin-dependent protein kinase type II subunit beta
B: Calcium/calmodulin-dependent protein kinase type II subunit beta
C: Calcium/calmodulin-dependent protein kinase type II subunit beta

G: Calcium/calmodulin-dependent protein kinase type II subunit beta
A: Calcium/calmodulin-dependent protein kinase type II subunit beta
B: Calcium/calmodulin-dependent protein kinase type II subunit beta
C: Calcium/calmodulin-dependent protein kinase type II subunit beta


Theoretical massNumber of molelcules
Total (without water)249,41716
Polymers249,41716
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area35190 Å2
ΔGint-260 kcal/mol
Surface area82560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.343, 81.343, 180.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 15588.548 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2B, CAM2, CAMK2, CAMKB / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q13554, Ca2+/calmodulin-dependent protein kinase

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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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M imidazole pH 7, 0.15 M DL-Malic acid, 22% PEG methyl ether 550

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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: 1.54178 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Mar 9, 2020 / Details: Rigaku VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.45→60 Å / Num. obs: 8502 / % possible obs: 99.2 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.368 / Rpim(I) all: 0.154 / Rrim(I) all: 0.403 / Χ2: 4.508 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.47-3.537.51.2734150.650.4621.3611.54599
3.53-3.597.50.8554120.6680.3080.9131.74899.5
3.59-3.667.90.7674000.7070.2730.8171.93499.3
3.66-3.747.51.3434180.7260.4831.4331.8399.5
3.74-3.827.81.2334070.7820.4451.3161.75100
3.82-3.917.70.9494250.7910.3451.0142.18299.3
3.91-4.017.90.6973980.8730.2530.7442.038100
4.01-4.117.70.7374260.8770.2680.7872.371100
4.11-4.237.80.7054140.8810.2840.7643.41899.5
4.23-4.377.40.7854230.0820.4930.9445.24199.8
4.37-4.537.30.4524210.930.1670.4843.49799.3
4.53-4.717.30.4564120.8540.1710.4895.75299.8
4.71-4.927.30.3054330.9470.1140.3275.28100
4.92-5.187.10.3764250.9420.1390.4033.7299.1
5.18-5.517.30.3444330.9520.1250.3683.43899.1
5.51-5.937.10.4934190.8920.1840.5293.9599.5
5.93-6.537.10.2824380.9380.1070.3044.32699.8
6.53-7.476.80.2814450.9310.1080.3036.07499.6
7.47-9.416.60.164440.990.0640.17315.06497.8
9.41-606.40.1164940.9920.0470.12616.57895.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7URW

7urw


Resolution: 3.45→37.09 Å / Cor.coef. Fo:Fc: 0.812 / Cor.coef. Fo:Fc free: 0.712 / SU B: 61.406 / SU ML: 0.901 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.4074 424 5.1 %RANDOM
Rwork0.3516 ---
obs0.3544 7921 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.76 Å2 / Biso mean: 99.495 Å2 / Biso min: 75.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å2-0 Å2-0 Å2
2--0.49 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 3.45→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 0 0 3910
Num. residues----508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134013
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173476
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.6435471
X-RAY DIFFRACTIONr_angle_other_deg1.0561.5717971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2575502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24323.153222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45315555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0391519
X-RAY DIFFRACTIONr_chiral_restr0.0320.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024697
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02949
LS refinement shellResolution: 3.45→3.537 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.448 33 -
Rwork0.465 578 -
obs--98.71 %

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