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- EMDB-21868: Cryo-EM of the S. islandicus filamentous virus, SIFV -

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Basic information

Entry
Database: EMDB / ID: EMD-21868
TitleCryo-EM of the S. islandicus filamentous virus, SIFV
Map dataCryo-EM of the S. islandicus filamentous virus, SIFV
Sample
  • Virus: Sulfolobus islandicus filamentous virus
    • DNA: A-DNA
    • DNA: A-DNA
    • Protein or peptide: Structural protein MCP2
    • Protein or peptide: Structural protein MCP1
Keywordshelical symmetry / archaeal virus / rod-like virus / structural protein / VIRUS
Function / homologyhelical viral capsid / DNA binding / Major capsid protein 1 / Major capsid protein 2
Function and homology information
Biological speciesSulfolobus islandicus filamentous virus
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsWang F / Baquero DP
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments.
Authors: Fengbin Wang / Diana P Baquero / Leticia C Beltran / Zhangli Su / Tomasz Osinski / Weili Zheng / David Prangishvili / Mart Krupovic / Edward H Egelman /
Abstract: Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) ...Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) to solve the atomic structures of two filamentous double-stranded DNA viruses that infect archaeal hosts living in nearly boiling acid: rod-shaped virus 1 (SSRV1), at 2.8-Å resolution, and filamentous virus (SIFV), at 4.0-Å resolution. The SIFV nucleocapsid is formed by a heterodimer of two homologous proteins and is membrane enveloped, while SSRV1 has a nucleocapsid formed by a homodimer and is not enveloped. In both, the capsid proteins wrap around the DNA and maintain it in an A-form. We suggest that the A-form is due to both a nonspecific desolvation of the DNA by the protein, and a specific coordination of the DNA phosphate groups by positively charged residues. We extend these observations by comparisons with four other archaeal filamentous viruses whose structures we have previously determined, and show that all 10 capsid proteins (from four heterodimers and two homodimers) have obvious structural homology while sequence similarity can be nonexistent. This arises from most capsid residues not being under any strong selective pressure. The inability to detect homology at the sequence level arises from the sampling of viruses in this part of the biosphere being extremely sparse. Comparative structural and genomic analyses suggest that nonenveloped archaeal viruses have evolved from enveloped viruses by shedding the membrane, indicating that this trait may be relatively easily lost during virus evolution.
History
DepositionApr 28, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wq2
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wq2
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21868.png

Downloads & links

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Map

FileDownload / File: emd_21868.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of the S. islandicus filamentous virus, SIFV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 320 pix.
= 448. Å		1.4 Å/pix.
x 320 pix.
= 448. Å		1.4 Å/pix.
x 320 pix.
= 448. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0344 / Movie #1: 0.04
Minimum - Maximum-0.032653145 - 0.08471636
Average (Standard dev.)0.0029530034 (±0.008790001)
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 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z448.000448.000448.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.0330.0850.003

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Supplemental data

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Sample components

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Entire : Sulfolobus islandicus filamentous virus

EntireName: Sulfolobus islandicus filamentous virus
Components
  • Virus: Sulfolobus islandicus filamentous virus
    • DNA: A-DNA
    • DNA: A-DNA
    • Protein or peptide: Structural protein MCP2
    • Protein or peptide: Structural protein MCP1

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Supramolecule #1: Sulfolobus islandicus filamentous virus

SupramoleculeName: Sulfolobus islandicus filamentous virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 176106 / Sci species name: Sulfolobus islandicus filamentous virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Sulfolobus islandicus (acidophilic)

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Macromolecule #1: A-DNA

MacromoleculeName: A-DNA / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Sulfolobus islandicus filamentous virus
Molecular weightTheoretical: 69.416977 KDa
SequenceString: (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT) ...String:
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)

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Macromolecule #2: A-DNA

MacromoleculeName: A-DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Sulfolobus islandicus filamentous virus
Molecular weightTheoretical: 68.79057 KDa
SequenceString: (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DA) ...String:
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)

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Macromolecule #3: Structural protein MCP2

MacromoleculeName: Structural protein MCP2 / type: protein_or_peptide / ID: 3 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus filamentous virus
Molecular weightTheoretical: 18.901863 KDa
SequenceString:
MARRNRRLSS ASVYRYYLKR ISMNIGTTGH VNGLSIAGNP EIMRAIARLS EQETYNWVTD YAPSHLAKEV VKQISGKYNI PGAYQGLLM AFAEKVLANY ILDYKGEPLV EIHHNFLWEL MQRQSGAGLG VTSGFIYTFV RKDGKPVTVD MSKVLTEIED A LFKLVKK

UniProtKB: Major capsid protein 2

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Macromolecule #4: Structural protein MCP1

MacromoleculeName: Structural protein MCP1 / type: protein_or_peptide / ID: 4 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus filamentous virus
Molecular weightTheoretical: 22.557898 KDa
SequenceString: MAGRQSHKKI DVRNDTSTRY KGKLYGIFVN YMGEKYAQQL VENMYSNYND VFVEIYNKMH NALRPTLVKL AGAGATFPLW QLVNEAIYA VYLTHKETAS FLVTKYVARG VPAMTVKTLL AEVGNQLKEL VPAVAEQIGS VTLDHTNVVS TVDNIVTSMP A LPNSYAGV ...String:
MAGRQSHKKI DVRNDTSTRY KGKLYGIFVN YMGEKYAQQL VENMYSNYND VFVEIYNKMH NALRPTLVKL AGAGATFPLW QLVNEAIYA VYLTHKETAS FLVTKYVARG VPAMTVKTLL AEVGNQLKEL VPAVAEQIGS VTLDHTNVVS TVDNIVTSMP A LPNSYAGV LMKTKVPTVT PHYAGTGTFS SMESAYKALE DIERGL

UniProtKB: Major capsid protein 1

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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
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.48 Å
Applied symmetry - Helical parameters - Δ&Phi: 38.49 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: OTHER / Number images used: 167500
Startup modelType of model: OTHER
Details: averaged cylinder using all segments, with random azimuthal angles
Final angle assignmentType: NOT APPLICABLE

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