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- PDB-6tn7: Crystal structure of the human Arc C-lobe -

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Basic information

Entry
Database: PDB / ID: 6tn7
TitleCrystal structure of the human Arc C-lobe
ComponentsActivity-regulated cytoskeleton-associated protein
KeywordsPROTEIN BINDING / Arc / capsid homology
Function / homology
Function and homology information


postsynaptic endosome / virus-like capsid / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / clathrin-coated vesicle membrane / endoderm development / regulation of dendritic spine morphogenesis / NGF-stimulated transcription / dendritic spine morphogenesis / regulation of cell morphogenesis ...postsynaptic endosome / virus-like capsid / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / clathrin-coated vesicle membrane / endoderm development / regulation of dendritic spine morphogenesis / NGF-stimulated transcription / dendritic spine morphogenesis / regulation of cell morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / regulation of long-term synaptic potentiation / response to morphine / 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 / long-term synaptic potentiation / postsynaptic density membrane / modulation of chemical synaptic transmission / protein homooligomerization / endocytosis / extracellular vesicle / cell migration / actin cytoskeleton / cell cortex / early endosome membrane / response to ethanol / dendritic spine / membrane raft / mRNA binding / neuronal cell body / glutamatergic synapse / structural molecule activity / plasma membrane / cytosol / cytoplasm
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
Similarity search - Domain/homology
Activity-regulated cytoskeleton-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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 6, 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

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Assembly

Deposited unit
B: Activity-regulated cytoskeleton-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3582
Polymers11,2661
Non-polymers921
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area6130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.210, 38.290, 61.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-512-

HOH

21B-541-

HOH

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Components

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


Mass: 11265.796 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARC, KIAA0278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7LC44
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 16% PEG 8000, 40 mM KH2PO4, 20% glycerol

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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: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 9789 / % possible obs: 92.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 35.2 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.055 / Rsym value: 0.051 / Net I/σ(I): 18.3
Reflection shellResolution: 1.67→1.71 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 245 / CC1/2: 0.857 / Rrim(I) all: 0.699 / Rsym value: 0.626

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x3x

4x3x


Resolution: 1.67→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2681 -10 %
Rwork0.2415 --
obs-9746 92.06 %
Displacement parametersBiso mean: 51.75 Å2
Refinement stepCycle: LAST / Resolution: 1.67→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms730 0 6 46 782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037747
X-RAY DIFFRACTIONf_angle_d0.76851007
X-RAY DIFFRACTIONf_chiral_restr0.0317110
X-RAY DIFFRACTIONf_plane_restr0.0035133
X-RAY DIFFRACTIONf_dihedral_angle_d22.6812468

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