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- PDB-6gse: Solution structure of the capsid domain from the activity-regulat... -

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Basic information

Entry
Database: PDB / ID: 6gse
TitleSolution structure of the capsid domain from the activity-regulated cytoskeleton-associated protein, Arc
ComponentsActivity-regulated cytoskeleton-associated protein
KeywordsPROTEIN BINDING / retroviral capsid domain / NMDA receptor interaction / Gag protein
Function / homology
Function and homology information


postsynaptic endosome / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / clathrin-coated vesicle membrane / endoderm development / regulation of dendritic spine morphogenesis / regulation of cell morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / response to morphine / positive regulation of AMPA receptor activity ...postsynaptic endosome / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / clathrin-coated vesicle membrane / endoderm development / regulation of dendritic spine morphogenesis / regulation of cell morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / response to morphine / positive regulation of AMPA receptor activity / regulation of long-term synaptic potentiation / anterior/posterior pattern specification / regulation of long-term synaptic depression / regulation of neuronal synaptic plasticity / mRNA transport / long-term memory / cytoskeleton organization / acrosomal vesicle / learning / postsynaptic density membrane / modulation of chemical synaptic transmission / protein homooligomerization / endocytosis / extracellular vesicle / actin cytoskeleton / cell migration / cell cortex / early endosome membrane / response to ethanol / dendritic spine / membrane raft / mRNA binding / glutamatergic synapse / dendrite / 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
Similarity search - Domain/homology
Activity-regulated cytoskeleton-associated protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing
AuthorsNielsen, L.D. / Erlendsson, S. / Teilum, K.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Other private Denmark
Other privateR151-2013-14302 Denmark
CitationJournal: Structure / Year: 2019
Title: The Capsid Domain of Arc Changes Its Oligomerization Propensity through Direct Interaction with the NMDA Receptor.
Authors: Nielsen, L.D. / Pedersen, C.P. / Erlendsson, S. / Teilum, K.
History
DepositionJun 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 21, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activity-regulated cytoskeleton-associated protein


Theoretical massNumber of molelcules
Total (without water)18,9961
Polymers18,9961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11450 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 18996.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arc / Production host: Escherichia coli (E. coli) / References: UniProt: Q63053

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic32D 1H-15N HSQC
122isotropic23D HNCA
132isotropic23D HN(CO)CA
142isotropic23D HNCO
152isotropic23D HN(CA)CO
162isotropic23D CBCA(CO)NH
172isotropic23D HN(CA)CB
182isotropic33D 1H-15N TOCSY
192isotropic33D (H)CCH-TOCSY
1102isotropic33D 1H-15N NOESY
1112isotropic33D 1H-13C NOESY
1122isotropic33D 1H-13C TOCSY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.5 mM [U-15N] Arc, 90% H2O/10% D2O15N90% H2O/10% D2O
solution21 mM [U-13C; U-15N] Arc, 90% H2O/10% D2O13C-15N90% H2O/10% D2O
solution30.5 mM [U-15N] Arc, 90% H2O/10% D2O15N-RDC90% H2O/10% D2OAligned in with lambda1 phages
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMArc[U-15N]1
1 mMArc[U-13C; U-15N]2
0.5 mMArc[U-15N]3
Sample conditionsIonic strength: 50 mM / Label: Normal / pH: 7.4 / Pressure: 1 bar / Temperature: 298 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III7502cryo-probe
Agilent DD2AgilentDD28003RT-probe

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CcpNmr AnalysisCCPNchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20

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