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- PDB-4x3h: CRYSTAL STRUCTURE OF ARC N-LOBE COMPLEXED WITH STARGAZIN PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 4x3h
TitleCRYSTAL STRUCTURE OF ARC N-LOBE COMPLEXED WITH STARGAZIN PEPTIDE
Components
  • Activity-regulated cytoskeleton-associated protein
  • VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-2 SUBUNIT
KeywordsSIGNALING PROTEIN / ENDOCYTOSIS MEDIATOR
Function / homology
Function and homology information


postsynaptic endosome / vesicle-mediated intercellular transport / Presynaptic depolarization and calcium channel opening / LGI-ADAM interactions / regulation of postsynaptic neurotransmitter receptor activity / neuronal ribonucleoprotein granule / Trafficking of AMPA receptors / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / clathrin-coated vesicle membrane ...postsynaptic endosome / vesicle-mediated intercellular transport / Presynaptic depolarization and calcium channel opening / LGI-ADAM interactions / regulation of postsynaptic neurotransmitter receptor activity / neuronal ribonucleoprotein granule / Trafficking of AMPA receptors / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / clathrin-coated vesicle membrane / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / endoderm development / regulation of dendritic spine morphogenesis / regulation of AMPA receptor activity / neurotransmitter receptor internalization / membrane hyperpolarization / postsynaptic neurotransmitter receptor diffusion trapping / nervous system process / regulation of cell morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / response to morphine / positive regulation of AMPA receptor activity / protein targeting to membrane / regulation of long-term synaptic potentiation / anterior/posterior pattern specification / voltage-gated calcium channel complex / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of long-term synaptic depression / neuromuscular junction development / transmission of nerve impulse / channel regulator activity / regulation of neuronal synaptic plasticity / regulation of postsynaptic membrane neurotransmitter receptor levels / membrane depolarization / AMPA glutamate receptor complex / voltage-gated calcium channel activity / mRNA transport / long-term memory / cytoskeleton organization / somatodendritic compartment / ionotropic glutamate receptor binding / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / acrosomal vesicle / regulation of membrane potential / learning / postsynaptic density membrane / modulation of chemical synaptic transmission / protein homooligomerization / Schaffer collateral - CA1 synapse / response to calcium ion / endocytosis / extracellular vesicle / actin cytoskeleton / cell migration / cell cortex / early endosome membrane / response to ethanol / dendritic spine / membrane raft / mRNA binding / glutamatergic synapse / dendrite / cell surface / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Activity-regulated cytoskeleton-associated protein, capsid domain / Activity-regulated cytoskeleton-associated protein, N-terminal domain / Arc MA domain / Activity-regulated cytoskeleton-associated protein / Activity-regulated cytoskeleton-associated protein, C-terminal domain / Arc C-lobe / Voltage-dependent calcium channel, gamma-2 subunit / : / PMP-22/EMP/MP20/Claudin family ...: / Activity-regulated cytoskeleton-associated protein, capsid domain / Activity-regulated cytoskeleton-associated protein, N-terminal domain / Arc MA domain / Activity-regulated cytoskeleton-associated protein / Activity-regulated cytoskeleton-associated protein, C-terminal domain / Arc C-lobe / Voltage-dependent calcium channel, gamma-2 subunit / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily
Similarity search - Domain/homology
Voltage-dependent calcium channel gamma-2 subunit / Activity-regulated cytoskeleton-associated protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.401 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 1.1Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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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: VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-2 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)10,6232
Polymers10,6232
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-7 kcal/mol
Surface area5710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.317, 54.317, 69.555
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-328-

HOH

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Components

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


Mass: 9346.333 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 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-2 SUBUNIT / NEURONAL VOLTAGE-GATED CALCIUM CHANNEL GAMMA-2 SUBUNIT / STARGAZIN / TRANSMEMBRANE AMPAR REGULATORY ...NEURONAL VOLTAGE-GATED CALCIUM CHANNEL GAMMA-2 SUBUNIT / STARGAZIN / TRANSMEMBRANE AMPAR REGULATORY PROTEIN GAMMA-2 / TARP GAMMA-2


Mass: 1276.468 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 225-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CACNG2, STG / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O88602*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M POTASSIUM SULFATE, 20% PEG 3350 AND 0.1 M MES , PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.401→25.298 Å / Num. obs: 4894 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Net I/σ(I): 4.9
Reflection shellResolution: 2.4→2.49 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.401→25.298 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 228 4.66 %
Rwork0.211 --
obs0.213 4894 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.401→25.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 0 0 53 806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018779
X-RAY DIFFRACTIONf_angle_d1.6581050
X-RAY DIFFRACTIONf_dihedral_angle_d18.724290
X-RAY DIFFRACTIONf_chiral_restr0.10994
X-RAY DIFFRACTIONf_plane_restr0.007137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4006-3.02380.26921150.23052284X-RAY DIFFRACTION100
3.0238-25.29980.23281130.20322382X-RAY DIFFRACTION99

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