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- PDB-7b55: Crystal structure of CaMKII-actinin complex bound to MES -

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Basic information

Entry
Database: PDB / ID: 7b55
TitleCrystal structure of CaMKII-actinin complex bound to MES
Components
  • Alpha-actinin-2
  • Calcium/calmodulin-dependent protein kinase type II subunit alpha
KeywordsSTRUCTURAL PROTEIN / CaMKII / actinin / dendritic spine
Function / homology
Function and homology information


regulation of synaptic vesicle docking / actin filament uncapping / FATZ binding / titin Z domain binding / HSF1-dependent transactivation / Interferon gamma signaling / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation ...regulation of synaptic vesicle docking / actin filament uncapping / FATZ binding / titin Z domain binding / HSF1-dependent transactivation / Interferon gamma signaling / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of potassium ion transmembrane transporter activity / regulation of endocannabinoid signaling pathway / RAF activation / calcium- and calmodulin-dependent protein kinase complex / Trafficking of AMPA receptors / Ca2+ pathway / RAF/MAP kinase cascade / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / Ca2+/calmodulin-dependent protein kinase / positive regulation of cation channel activity / LIM domain binding / regulation of neurotransmitter secretion / microspike assembly / regulation of neuron migration / negative regulation of hydrolase activity / dendritic spine development / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / positive regulation of potassium ion transport / Ion homeostasis / muscle cell development / focal adhesion assembly / positive regulation of calcium ion transport / Striated Muscle Contraction / calcium/calmodulin-dependent protein kinase activity / Nephrin family interactions / Assembly and cell surface presentation of NMDA receptors / regulation of mitochondrial membrane permeability involved in apoptotic process / cardiac muscle cell development / structural constituent of muscle / dendrite morphogenesis / sarcomere organization / cortical actin cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of potassium ion transport / pseudopodium / regulation of neuronal synaptic plasticity / Long-term potentiation / postsynaptic density, intracellular component / glutamate receptor binding / cellular response to interferon-beta / positive regulation of cardiac muscle cell apoptotic process / cytoskeletal protein binding / titin binding / phosphatidylinositol-4,5-bisphosphate binding / Ras activation upon Ca2+ influx through NMDA receptor / : / platelet alpha granule lumen / filopodium / regulation of membrane potential / cell projection / response to ischemia / protein localization to plasma membrane / actin filament / positive regulation of receptor signaling pathway via JAK-STAT / postsynaptic density membrane / Schaffer collateral - CA1 synapse / Z disc / G1/S transition of mitotic cell cycle / calcium ion transport / actin filament binding / integrin binding / cell junction / Platelet degranulation / actin cytoskeleton organization / RAF/MAP kinase cascade / regulation of apoptotic process / dendritic spine / transmembrane transporter binding / cytoskeleton / calmodulin binding / postsynaptic density / cell adhesion / protein domain specific binding / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / calcium ion binding / synapse / glutamatergic synapse / mitochondrion / extracellular exosome / extracellular region / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / NTF2-like domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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 alpha / Alpha-actinin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhu, J. / Gold, M.
CitationJournal: To Be Published
Title: Crystal structure of CaMKII-actinin complex bound to MES
Authors: Zhu, J. / Gold, M.
History
DepositionDec 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
A: Alpha-actinin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1984
Polymers43,8072
Non-polymers3902
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-3 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.574, 70.023, 91.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 35903.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Camk2a / Production host: Escherichia coli (E. coli)
References: UniProt: P11798, Ca2+/calmodulin-dependent protein kinase
#2: Protein Alpha-actinin-2 / Alpha-actinin skeletal muscle isoform 2 / F-actin cross-linking protein


Mass: 7903.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P35609
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 20% w/v PEG4000, 0.2 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.6→91.32 Å / Num. obs: 57062 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 31.35 Å2 / CC1/2: 1 / Rpim(I) all: 0.018 / Net I/σ(I): 14.6
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2778 / CC1/2: 0.639 / Rpim(I) all: 0.783

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VZ6

2vz6


Resolution: 1.6→55.57 Å / SU ML: 0.2062 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8893
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 1999 3.52 %
Rwork0.1972 54840 -
obs0.1979 56839 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.7 Å2
Refinement stepCycle: LAST / Resolution: 1.6→55.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 24 383 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573021
X-RAY DIFFRACTIONf_angle_d0.80674102
X-RAY DIFFRACTIONf_chiral_restr0.0498452
X-RAY DIFFRACTIONf_plane_restr0.0052527
X-RAY DIFFRACTIONf_dihedral_angle_d24.78471117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.43711490.39333813X-RAY DIFFRACTION99.03
1.64-1.680.37861330.36163850X-RAY DIFFRACTION99.35
1.68-1.730.39481270.33683850X-RAY DIFFRACTION99.45
1.73-1.790.31551500.30763888X-RAY DIFFRACTION99.61
1.79-1.850.30591370.26923876X-RAY DIFFRACTION99.5
1.85-1.930.24991390.22953873X-RAY DIFFRACTION99.78
1.93-2.020.26121420.21723921X-RAY DIFFRACTION99.71
2.02-2.120.22821520.21213860X-RAY DIFFRACTION99.8
2.12-2.260.20831350.19783930X-RAY DIFFRACTION100
2.26-2.430.22881410.19323911X-RAY DIFFRACTION99.98
2.43-2.670.22871480.20233938X-RAY DIFFRACTION100
2.67-3.060.19551470.20563964X-RAY DIFFRACTION100
3.06-3.860.18451460.17943997X-RAY DIFFRACTION100
3.86-55.570.19481530.17164169X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 15.9133667869 Å / Origin y: -5.11448531575 Å / Origin z: -2.38755678608 Å
111213212223313233
T0.273509776339 Å2-0.0211697118281 Å2-0.00258963152978 Å2-0.272359909732 Å20.0063500309647 Å2--0.310059368488 Å2
L0.786900295193 °2-0.283696648336 °20.0326005293311 °2-0.623411420958 °2-0.308583073733 °2--1.21115711642 °2
S-0.00995234598275 Å °-0.00340460515805 Å °-0.0523445181488 Å °-0.0102198823682 Å °-0.00169631571947 Å °-0.0356238048106 Å °-0.0511228481036 Å °0.0565533274189 Å °0.000655019141049 Å °
Refinement TLS groupSelection details: all

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