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- PDB-6s7x: dARC1 capsid domain dimer, orthorhombic form at 1.7 Angstrom -

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Basic information

Entry
Database: PDB / ID: 6s7x
TitledARC1 capsid domain dimer, orthorhombic form at 1.7 Angstrom
ComponentsActivity-regulated cytoskeleton associated protein 1
KeywordsNEUROPEPTIDE / Capsid Retrotransposon Trafficking Exapted
Function / homology
Function and homology information


postsynapse of neuromuscular junction / muscle system process / behavioral response to starvation / virus-like capsid / vesicle-mediated intercellular transport / regulation of neuronal synaptic plasticity / mRNA transport / sarcomere / extracellular vesicle / mRNA binding ...postsynapse of neuromuscular junction / muscle system process / behavioral response to starvation / virus-like capsid / vesicle-mediated intercellular transport / regulation of neuronal synaptic plasticity / mRNA transport / sarcomere / extracellular vesicle / mRNA binding / synapse / structural molecule activity / identical protein binding / membrane
Similarity search - Function
Activity-regulated cytoskeleton associated protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsCottee, M.A. / Taylor, I.A.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Cancer Research UKFC001162, FC001178 United Kingdom
Medical Research Council (United Kingdom)FC001162, FC001178 United Kingdom
Wellcome TrustFC001162, FC001178 United Kingdom
Wellcome Trust108014/Z/15/Z United Kingdom
Wellcome Trust108012/Z/15/Z United Kingdom
CitationJournal: Sci Adv / Year: 2020
Title: Structure ofDrosophila melanogasterARC1 reveals a repurposed molecule with characteristics of retroviral Gag.
Authors: Cottee, M.A. / Letham, S.C. / Young, G.R. / Stoye, J.P. / Taylor, I.A.
History
DepositionJul 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activity-regulated cytoskeleton associated protein 1
B: Activity-regulated cytoskeleton associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6647
Polymers39,5122
Non-polymers1525
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Only witnessed as a dimer, light scattering, MALLS. Only witnessed as a dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-59 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.334, 70.386, 142.821
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A43 - 204
2010B43 - 204

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Components

#1: Protein Activity-regulated cytoskeleton associated protein 1 / dArc1


Mass: 19755.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Arc1, CG12505 / Plasmid: pET22b / Details (production host): NdeI XhoI / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q7K1U0
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 70.04 % / Description: Rodlike, ~400x30x30
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NaCl 2.8-3.3 M, 0.1 M HEPES pH 7.5 / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.98399 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98399 Å / Relative weight: 1
ReflectionResolution: 1.55→71.41 Å / Num. obs: 48232 / % possible obs: 84.1 % / Redundancy: 10 % / CC1/2: 0.998 / Rpim(I) all: 0.029 / Rrim(I) all: 0.093 / Net I/σ(I): 10.3
Reflection shellResolution: 1.55→1.7 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2412 / CC1/2: 0.557 / Rpim(I) all: 0.478 / Rrim(I) all: 1.501 / % possible all: 66

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Processing

Software
NameVersionClassification
AutoPROC1.0.5data scaling
XDSJan 26, 2018 (BUILT 20180409)data reduction
XSCALEJan 26, 2018 (BUILT 20180409)data scaling
pointless1.11.12data scaling
Aimless0.7.1data scaling
TRUNCATE1.17.29data reduction
STARANISO1.10.15 (20180503)data scaling
AutoSol1.14_3260phasing
BUCCANEER1.5model building
Coot0.8.9.2model building
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.7→71.41 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.979 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.114
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 2241 4.9 %RANDOM
Rwork0.1808 ---
obs0.1824 43484 65.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.45 Å2 / Biso mean: 22.124 Å2 / Biso min: 10.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.7→71.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 5 391 3077
Biso mean--33.17 31.55 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132804
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172513
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.6413797
X-RAY DIFFRACTIONr_angle_other_deg1.4981.5795850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7515342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.76222.865171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94615482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9371517
X-RAY DIFFRACTIONr_chiral_restr0.0780.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023175
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02624
Refine LS restraints NCS

Ens-ID: 1 / Number: 5151 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 69 -
Rwork0.252 1680 -
all-1749 -
obs--34.27 %

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