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- PDB-6tno: Crystal structure of the human Arc N-lobe bound to stargazin -

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Basic information

Entry
Database: PDB / ID: 6tno
TitleCrystal structure of the human Arc N-lobe bound to stargazin
Components
  • Arc_C domain-containing protein
  • Chains: B,D,F
KeywordsPROTEIN BINDING / Arc / capsid homology
Function / homology
Function and homology information


LGI-ADAM interactions / neuronal ribonucleoprotein granule / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / Presynaptic depolarization and calcium channel opening / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / endoderm development / regulation of AMPA receptor activity / neurotransmitter receptor internalization ...LGI-ADAM interactions / neuronal ribonucleoprotein granule / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / Presynaptic depolarization and calcium channel opening / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / endoderm development / regulation of AMPA receptor activity / neurotransmitter receptor internalization / channel regulator activity / membrane hyperpolarization / Trafficking of AMPA receptors / postsynaptic neurotransmitter receptor diffusion trapping / regulation of cell morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / regulation of long-term synaptic potentiation / protein targeting to membrane / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of AMPA receptor activity / voltage-gated calcium channel complex / anterior/posterior pattern specification / neuromuscular junction development / regulation of long-term synaptic depression / transmission of nerve impulse / regulation of neuronal synaptic plasticity / membrane depolarization / AMPA glutamate receptor complex / voltage-gated calcium channel activity / long-term memory / somatodendritic compartment / cytoskeleton organization / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / response to calcium ion / endocytic vesicle membrane / cell migration / actin cytoskeleton / dendritic spine / membrane raft / glutamatergic synapse / cell surface / plasma membrane / cytoplasm
Similarity search - Function
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
Arc_C domain-containing protein / Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesFelis catus (domestic cat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHallin, E.I. / Bramham, C.R. / Kursula, P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norwegian Research Council249951 Norway
CitationJournal: Biochem Biophys Rep / Year: 2021
Title: Structural properties and peptide ligand binding of the capsid homology domains of human Arc.
Authors: Hallin, E.I. / Bramham, C.R. / Kursula, P.
History
DepositionDec 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Arc_C domain-containing protein
B: Chains: B,D,F
C: Arc_C domain-containing protein
D: Chains: B,D,F
E: Arc_C domain-containing protein
F: Chains: B,D,F


Theoretical massNumber of molelcules
Total (without water)29,9316
Polymers29,9316
Non-polymers00
Water1,928107
1
A: Arc_C domain-containing protein
B: Chains: B,D,F


Theoretical massNumber of molelcules
Total (without water)9,9772
Polymers9,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-6 kcal/mol
Surface area4780 Å2
MethodPISA
2
C: Arc_C domain-containing protein
D: Chains: B,D,F


Theoretical massNumber of molelcules
Total (without water)9,9772
Polymers9,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-5 kcal/mol
Surface area4760 Å2
MethodPISA
3
E: Arc_C domain-containing protein
F: Chains: B,D,F


Theoretical massNumber of molelcules
Total (without water)9,9772
Polymers9,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-5 kcal/mol
Surface area4990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.390, 29.770, 71.790
Angle α, β, γ (deg.)90.000, 92.510, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Arc_C domain-containing protein


Mass: 8863.826 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: ARC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I2UQ80
#2: Protein/peptide Chains: B,D,F


Mass: 1113.295 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: peptide from stargazin / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y698*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.83 Å3/Da / Density % sol: 32.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 1.4 M trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 17135 / % possible obs: 97.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 36.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.048 / Rsym value: 0.041 / Net I/σ(I): 18.6
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1246 / CC1/2: 0.921 / Rrim(I) all: 0.451 / Rsym value: 0.386 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x3h

4x3h


Resolution: 1.9→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2161 -10 %
Rwork0.1819 --
obs-17109 97.8 %
Displacement parametersBiso mean: 45.87 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 0 107 2064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542042
X-RAY DIFFRACTIONf_angle_d0.88452751
X-RAY DIFFRACTIONf_chiral_restr0.0474247
X-RAY DIFFRACTIONf_plane_restr0.006357
X-RAY DIFFRACTIONf_dihedral_angle_d20.92181180

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