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- PDB-7b56: Crystal structure of CaMKII-actinin complex bound to AMPPNP -

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Basic information

Entry
Database: PDB / ID: 7b56
TitleCrystal structure of CaMKII-actinin complex bound to AMPPNP
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 / positive regulation of potassium ion transmembrane transporter activity / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling / Ion transport by P-type ATPases ...regulation of synaptic vesicle docking / actin filament uncapping / FATZ binding / titin Z domain binding / HSF1-dependent transactivation / Interferon gamma signaling / positive regulation of potassium ion transmembrane transporter activity / 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 / regulation of endocannabinoid signaling pathway / RAF activation / calcium- and calmodulin-dependent protein kinase complex / Trafficking of AMPA receptors / Ca2+ pathway / RAF/MAP kinase cascade / Ca2+/calmodulin-dependent protein kinase / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / positive regulation of cation channel activity / LIM domain binding / microspike assembly / negative regulation of hydrolase activity / dendritic spine development / regulation of neuron migration / regulation of neurotransmitter secretion / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / positive regulation of potassium ion transport / Ion homeostasis / focal adhesion assembly / muscle cell development / 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 / pseudopodium / negative regulation of potassium ion transport / 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 / response to ischemia / protein localization to plasma membrane / regulation of membrane potential / cell projection / positive regulation of receptor signaling pathway via JAK-STAT / filopodium / actin filament / 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 / synapse / calcium ion binding / glutamatergic synapse / mitochondrion / extracellular exosome / extracellular region / ATP binding / metal ion binding / identical protein 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 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: 1.45 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)44,5335
Polymers43,8072
Non-polymers7263
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-21 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.426, 72.510, 92.001
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

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Protein , 2 types, 2 molecules BA

#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

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Non-polymers , 4 types, 444 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.85 %
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: 1.45→92 Å / Num. obs: 77065 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 22.55 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.016 / Net I/σ(I): 18.5
Reflection shellResolution: 1.45→1.47 Å / Num. unique obs: 3786 / CC1/2: 0.825 / Rpim(I) all: 0.522

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Processing

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

2vz6


Resolution: 1.45→52.77 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2154 1996 2.6 %
Rwork0.1901 74889 -
obs0.1908 76885 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.22 Å2
Refinement stepCycle: LAST / Resolution: 1.45→52.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 44 441 3385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573049
X-RAY DIFFRACTIONf_angle_d0.97424149
X-RAY DIFFRACTIONf_chiral_restr0.0763456
X-RAY DIFFRACTIONf_plane_restr0.0058529
X-RAY DIFFRACTIONf_dihedral_angle_d25.08671121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.28411400.28455283X-RAY DIFFRACTION99.69
1.49-1.530.23621400.24945259X-RAY DIFFRACTION99.7
1.53-1.570.23951420.2265300X-RAY DIFFRACTION99.67
1.57-1.620.24291400.21135259X-RAY DIFFRACTION99.58
1.62-1.680.23151410.20595292X-RAY DIFFRACTION99.72
1.68-1.750.26571420.21665313X-RAY DIFFRACTION99.73
1.75-1.830.21811410.20265302X-RAY DIFFRACTION99.83
1.83-1.920.23651420.19655294X-RAY DIFFRACTION99.89
1.92-2.040.20961420.19235356X-RAY DIFFRACTION99.91
2.04-2.20.22751430.19395359X-RAY DIFFRACTION100
2.2-2.420.18491430.19085374X-RAY DIFFRACTION100
2.42-2.770.25631440.20125398X-RAY DIFFRACTION99.96
2.77-3.490.20671450.18695436X-RAY DIFFRACTION100
3.49-52.770.19971510.17175664X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 15.1121581365 Å / Origin y: -5.04463431322 Å / Origin z: -2.5044161769 Å
111213212223313233
T0.155220329519 Å2-0.00909408337564 Å20.0156327723026 Å2-0.17085218412 Å2-0.01153362473 Å2--0.1753018623 Å2
L0.4910913964 °2-0.044831707403 °20.236917221921 °2-0.406183786294 °2-0.149582352756 °2--0.728566639229 °2
S-0.00983201735945 Å °0.0262968054646 Å °-0.0150357802084 Å °0.0277117250096 Å °0.0342016859214 Å °-0.0299469579307 Å °-0.0709124387588 Å °0.103534743467 Å °-1.39634220456E-6 Å °
Refinement TLS groupSelection details: all

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