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- PDB-4x3i: The crystal structure of Arc N-lobe complexed with CAMK2A fragment -

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Basic information

Entry
Database: PDB / ID: 4x3i
TitleThe crystal structure of Arc N-lobe complexed with CAMK2A fragment
Components
  • Activity-regulated cytoskeleton-associated protein
  • CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II SUBUNIT ALPHA
KeywordsSIGNALING PROTEIN / ENDOCYTOSIS MEDIATOR
Function / homology
Function and homology information


regulation of synaptic vesicle docking / positive regulation of AMPA receptor activity / HSF1-dependent transactivation / Interferon gamma signaling / virus-like capsid / vesicle-mediated intercellular transport / peptidyl-threonine autophosphorylation / postsynaptic endosome / Ion transport by P-type ATPases / neuronal ribonucleoprotein granule ...regulation of synaptic vesicle docking / positive regulation of AMPA receptor activity / HSF1-dependent transactivation / Interferon gamma signaling / virus-like capsid / vesicle-mediated intercellular transport / peptidyl-threonine autophosphorylation / postsynaptic endosome / Ion transport by P-type ATPases / neuronal ribonucleoprotein granule / RAF activation / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / neurotransmitter receptor transport to plasma membrane / Unblocking of NMDA receptors, glutamate binding and activation / Ca2+ pathway / Trafficking of AMPA receptors / Ca2+/calmodulin-dependent protein kinase / RAF/MAP kinase cascade / negative regulation of hydrolase activity / dendritic spine development / clathrin-coated vesicle membrane / regulation of neurotransmitter secretion / endoderm development / regulation of dendritic spine morphogenesis / Ion homeostasis / positive regulation of calcium ion transport / regulation of neuron migration / calcium/calmodulin-dependent protein kinase activity / regulation of long-term synaptic potentiation / regulation of cell morphogenesis / regulation of mitochondrial membrane permeability involved in apoptotic process / anterior/posterior pattern specification / GTPase activating protein binding / dendrite morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / response to morphine / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of ferroptosis / regulation of neuronal synaptic plasticity / glutamate receptor binding / mRNA transport / postsynaptic cytosol / long-term memory / cell surface receptor signaling pathway via JAK-STAT / regulation of protein localization to plasma membrane / presynaptic cytosol / cellular response to interferon-beta / regulation of long-term synaptic depression / cytoskeleton organization / positive regulation of cardiac muscle cell apoptotic process / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / acrosomal vesicle / response to ischemia / angiotensin-activated signaling pathway / learning / positive regulation of receptor signaling pathway via JAK-STAT / response to cocaine / G1/S transition of mitotic cell cycle / protein homooligomerization / postsynaptic density membrane / cellular response to type II interferon / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / endocytosis / kinase activity / calcium ion transport / cell migration / extracellular vesicle / actin cytoskeleton / early endosome membrane / cell cortex / dendritic spine / response to ethanol / calmodulin binding / neuron projection / postsynaptic density / membrane raft / axon / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / mRNA binding / synapse / dendrite / glutamatergic synapse / structural molecule activity / protein homodimerization activity / mitochondrion / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Activity-regulated cytoskeleton-associated protein, capsid domain / Activity-regulated cytoskeleton-associated protein / Activity-regulated cytoskeleton-associated protein, C-terminal domain / Activity-regulated cytoskeleton-associated protein, N-terminal domain / Arc C-lobe / Arc MA domain / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily ...: / Activity-regulated cytoskeleton-associated protein, capsid domain / Activity-regulated cytoskeleton-associated protein / Activity-regulated cytoskeleton-associated protein, C-terminal domain / Activity-regulated cytoskeleton-associated protein, N-terminal domain / Arc C-lobe / Arc MA domain / 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 alpha / Activity-regulated cytoskeleton-associated protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, W. / Ward, M. / Leahy, D. / Worley, P.
CitationJournal: Neuron / Year: 2015
Title: Structural basis of arc binding to synaptic proteins: implications for cognitive disease.
Authors: Zhang, W. / Wu, J. / Ward, M.D. / Yang, S. / Chuang, Y.A. / Xiao, M. / Li, R. / Leahy, D.J. / Worley, P.F.
History
DepositionNov 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _struct_keywords.text
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Activity-regulated cytoskeleton-associated protein
B: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II SUBUNIT ALPHA


Theoretical massNumber of molelcules
Total (without water)10,1462
Polymers10,1462
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-4 kcal/mol
Surface area5000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.527, 51.527, 69.929
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Activity-regulated cytoskeleton-associated protein / ARC/ARG3.1 / Activity-regulated gene 3.1 protein / Arg3.1


Mass: 9393.229 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 207-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arc / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q63053
#2: Protein/peptide CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II SUBUNIT ALPHA / CAM KINASE II SUBUNIT ALPHA / CAMK-II SUBUNIT ALPHA


Mass: 752.797 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 309-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CAMK2A / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P11798*PLUS, Ca2+/calmodulin-dependent protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2M AMMONIUM SULFATE AND 0.1 M TRIS, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9801 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.8→25.763 Å / Num. obs: 9807 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Net I/σ(I): 10.3
Reflection shellHighest resolution: 1.8 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→25.76 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 471 4.8 %
Rwork0.194 --
obs0.195 9807 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→25.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 0 0 70 740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007701
X-RAY DIFFRACTIONf_angle_d0.993946
X-RAY DIFFRACTIONf_dihedral_angle_d15.652257
X-RAY DIFFRACTIONf_chiral_restr0.07287
X-RAY DIFFRACTIONf_plane_restr0.004124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7999-2.06030.23681550.18693098X-RAY DIFFRACTION100
2.0603-2.59540.23131510.20663111X-RAY DIFFRACTION100
2.5954-25.76610.18791650.19033127X-RAY DIFFRACTION100

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