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- PDB-6s7y: dARC1 capsid domain dimer, hexagonal form at 2.3 Angstrom -

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Basic information

Entry
Database: PDB / ID: 6s7y
TitledARC1 capsid domain dimer, hexagonal form at 2.3 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: 2.3 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
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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 1
B: Activity-regulated cytoskeleton associated protein 1


Theoretical massNumber of molelcules
Total (without water)39,5122
Polymers39,5122
Non-polymers00
Water36020
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 area2080 Å2
ΔGint-18 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.191, 62.191, 400.999
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 45 through 74 or resid 76...
21(chain B and (resid 45 through 74 or resid 76...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 45 through 74 or resid 76...A45 - 74
121(chain A and (resid 45 through 74 or resid 76...A76 - 79
131(chain A and (resid 45 through 74 or resid 76...A81 - 101
141(chain A and (resid 45 through 74 or resid 76...A45 - 204
151(chain A and (resid 45 through 74 or resid 76...A45 - 204
161(chain A and (resid 45 through 74 or resid 76...A137 - 148
171(chain A and (resid 45 through 74 or resid 76...A152 - 177
181(chain A and (resid 45 through 74 or resid 76...A179 - 185
191(chain A and (resid 45 through 74 or resid 76...A187 - 202
211(chain B and (resid 45 through 74 or resid 76...B45 - 74
221(chain B and (resid 45 through 74 or resid 76...B76 - 79
231(chain B and (resid 45 through 74 or resid 76...B81 - 101
241(chain B and (resid 45 through 74 or resid 76...B45 - 205
251(chain B and (resid 45 through 74 or resid 76...B137 - 148
261(chain B and (resid 45 through 74 or resid 76...B45 - 205
271(chain B and (resid 45 through 74 or resid 76...B150
281(chain B and (resid 45 through 74 or resid 76...B45 - 205
291(chain B and (resid 45 through 74 or resid 76...B152 - 177
2101(chain B and (resid 45 through 74 or resid 76...B0
2111(chain B and (resid 45 through 74 or resid 76...B187 - 202

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.98 Å3/Da / Density % sol: 58.77 % / Description: Hexagonal/Trapezoid Prism
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: 0.97941 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: 0.97941 Å / Relative weight: 1
ReflectionResolution: 2.14→57.29 Å / Num. obs: 26972 / % possible obs: 99.9 % / Redundancy: 40.8 % / Biso Wilson estimate: 38.445 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.025 / Rrim(I) all: 0.122 / Χ2: 0.83 / Net I/σ(I): 22
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 22.4 % / Rmerge(I) obs: 0.983 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1886 / CC1/2: 0.517 / Rpim(I) all: 0.298 / Rrim(I) all: 1.029 / % possible all: 99.3

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Processing

Software
NameVersionClassification
xia20.5.546-gdf2e053-dials-1.9data reduction
DIALS1.9.3-gb491019a-releasedata reduction
pointless1.11.12data scaling
Aimless0.7.1data scaling
BUCCANEER1.5model building
Coot0.8.9.2model building
TRUNCATE1.17.29data reduction
AutoSol1.14_3260phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.3→53.859 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 27.45
RfactorNum. reflection% reflection
Rfree0.2849 1844 4.79 %
Rwork0.2472 --
obs0.249 38529 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.18 Å2 / Biso mean: 65.0196 Å2 / Biso min: 27.51 Å2
Refinement stepCycle: final / Resolution: 2.3→53.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 0 20 2656
Biso mean---44.14 -
Num. residues----321
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A816X-RAY DIFFRACTION1.455TORSIONAL
12B816X-RAY DIFFRACTION1.455TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3-2.36220.31751210.31642798
2.3622-2.43170.32321400.30962825
2.4317-2.51020.29781490.28772844
2.5102-2.59990.3291210.29622845
2.5999-2.7040.35661310.30112871
2.704-2.82710.2991490.27522808
2.8271-2.97610.28961530.28552787
2.9761-3.16250.31011410.29682822
3.1625-3.40670.32991430.2752803
3.4067-3.74940.2591540.24022813
3.7494-4.29180.27091400.21112825
4.2918-5.40640.23031380.21022828
5.4064-53.8590.29531640.2162816
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00750.0020.00390.00280.00210.00650.0125-0.0599-0.0011-0.0155-0.04260.00060.0716-0.0259-0.00010.35120.1-0.02960.68290.01740.4109-39.13889.7847-22.9724
20.028-0.00810.00330.0093-0.0040.0019-0.0045-0.02040.04760.0111-0.00690.01-0.0052-0.0107-0.02260.18110.0144-0.00930.7911-0.10860.3634-29.101430.14687.9327
30.0034-0.00070.00460.00540.01460.05310.00520.0253-0.00490.0414-0.04230.02840.0767-0.01620.00460.2818-0.07430.06360.7367-0.06480.2964-8.290116.029426.1162
40.02650.0180.00770.01520.00620.0025-0.02380.00310.068-0.00370.00120.0012-0.01060.0321-0.0090.1697-0.0213-0.02170.7518-0.04460.308-16.914327.632-10.8246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 119 )A45 - 119
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 204 )A120 - 204
3X-RAY DIFFRACTION3chain 'B' and (resid 45 through 119 )B45 - 119
4X-RAY DIFFRACTION4chain 'B' and (resid 120 through 205 )B120 - 205

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