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- EMDB-26159: Cryo-EM of AFV6 -

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Basic information

Entry
Database: EMDB / ID: EMD-26159
TitleCryo-EM of AFV6
Map dataCryo-EM of AFV6
Sample
  • Virus: Acidianus filamentous virus 6
    • DNA: DNA (5'-D(*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*A)-3')
    • Protein or peptide: MCP1
    • Protein or peptide: MCP2
Keywordshelical symmetry / archaeal virus / VIRUS
Function / homologyStructural protein / Structural protein
Function and homology information
Biological speciesAcidianus filamentous virus 6
Methodhelical reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWang F / Cvirkaite-Krupovic V
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
CitationJournal: To Be Published
Title: Cryo-EM of AFV6
Authors: Wang F / Cvirkaite-Krupovic V / Krupovic M / Egelman EH
History
DepositionFeb 9, 2022-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26159.png

Downloads & links

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Map

FileDownload / File: emd_26159.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of AFV6
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.59
Minimum - Maximum-1.0442437 - 2.1205318
Average (Standard dev.)0.025935803 (±0.11298251)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 448.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Acidianus filamentous virus 6

EntireName: Acidianus filamentous virus 6
Components
  • Virus: Acidianus filamentous virus 6
    • DNA: DNA (5'-D(*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*A)-3')
    • Protein or peptide: MCP1
    • Protein or peptide: MCP2

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Supramolecule #1: Acidianus filamentous virus 6

SupramoleculeName: Acidianus filamentous virus 6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 346882 / Sci species name: Acidianus filamentous virus 6 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: DNA (5'-D(*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*A)-3')

MacromoleculeName: DNA (5'-D(*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*A)-3') / type: dna / ID: 1 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Acidianus filamentous virus 6
Molecular weightTheoretical: 3.65944 KDa
SequenceString:
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)

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Macromolecule #2: MCP1

MacromoleculeName: MCP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acidianus filamentous virus 6
Molecular weightTheoretical: 18.593428 KDa
SequenceString:
MAGKKRRLSQ ASVLRYYAKR FTMNVGTTAH VLGKEVAGNP WVAKAIDKLS YQETYNWISD YQASHLAKQV AKQVAEKYGI PPTFQGLLM AYAEKVVANY ILDYKGESLT QMHDNYLYEL MQKMPIAPTG TSSGYIYVFI GKDGKTHTVD MSKVLTDIED A LLKRA

UniProtKB: Structural protein

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Macromolecule #3: MCP2

MacromoleculeName: MCP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acidianus filamentous virus 6
Molecular weightTheoretical: 22.751678 KDa
SequenceString: MAGRQAHRKF DVRNDTSTRW KGKLYGIFVN YMGEDYAKEF VEQAYSNYEK VFVNIYTKIH NQLRTTLTSS AGAGATFPLW QIINEAIYA VYLTHKETAS FLYAKYVARG IQPNVVKKIL AETGNALKGI VPAVAQELGE TVLDESNVIS VVDDIVRKNP A LPNSYAGI ...String:
MAGRQAHRKF DVRNDTSTRW KGKLYGIFVN YMGEDYAKEF VEQAYSNYEK VFVNIYTKIH NQLRTTLTSS AGAGATFPLW QIINEAIYA VYLTHKETAS FLYAKYVARG IQPNVVKKIL AETGNALKGI VPAVAQELGE TVLDESNVIS VVDDIVRKNP A LPNSYAGI ILQEARISTT PHYEGTEGFS SMESAYSALE EIEKGL

UniProtKB: Structural protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.75 Å
Applied symmetry - Helical parameters - Δ&Phi: 38.46 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78141

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