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- EMDB-0299: Bacteriophage phi6 nucleocapsid reconstructed with icosahedral sy... -

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Basic information

Entry
Database: EMDB / ID: EMD-0299
TitleBacteriophage phi6 nucleocapsid reconstructed with icosahedral symmetry
Map dataBacteriophage phi6 nucleocapsid reconstructed with icosahedral symmetry
Sample
  • Virus: Pseudomonas phage phi6 (bacteriophage)
    • Protein or peptide: Major inner protein P1
    • Protein or peptide: Packaging Enzyme P4
    • Protein or peptide: Major Outer Capsid Protein P8
Function / homology: / Major inner capsid protein P1 / T=2 icosahedral viral capsid / viral inner capsid / viral nucleocapsid / RNA binding / identical protein binding / Major inner protein P1
Function and homology information
Biological speciesPseudomonas phage phi6 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsIlca SL / Huiskonen JT
CitationJournal: Nature / Year: 2019
Title: Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus.
Authors: Serban L Ilca / Xiaoyu Sun / Kamel El Omari / Abhay Kotecha / Felix de Haas / Frank DiMaio / Jonathan M Grimes / David I Stuart / Minna M Poranen / Juha T Huiskonen /
Abstract: Characterizing the genome of mature virions is pivotal to understanding the highly dynamic processes of virus assembly and infection. Owing to the different cellular fates of DNA and RNA, the life ...Characterizing the genome of mature virions is pivotal to understanding the highly dynamic processes of virus assembly and infection. Owing to the different cellular fates of DNA and RNA, the life cycles of double-stranded (ds)DNA and dsRNA viruses are dissimilar. In terms of nucleic acid packing, dsDNA viruses, which lack genome segmentation and intra-capsid transcriptional machinery, predominantly display single-spooled genome organizations. Because the release of dsRNA into the cytoplasm triggers host defence mechanisms, dsRNA viruses retain their genomes within a core particle that contains the enzymes required for RNA replication and transcription. The genomes of dsRNA viruses vary greatly in the degree of segmentation. In members of the Reoviridae family, genomes consist of 10-12 segments and exhibit a non-spooled arrangement mediated by RNA-dependent RNA polymerases. However, whether this arrangement is a general feature of dsRNA viruses remains unknown. Here, using cryo-electron microscopy to resolve the dsRNA genome structure of the tri-segmented bacteriophage ɸ6 of the Cystoviridae family, we show that dsRNA viruses can adopt a dsDNA-like single-spooled genome organization. We find that in this group of viruses, RNA-dependent RNA polymerases do not direct genome ordering, and the dsRNA can adopt multiple conformations. We build a model that encompasses 90% of the genome, and use this to quantify variation in the packing density and to characterize the different liquid crystalline geometries that are exhibited by the tightly compacted nucleic acid. Our results demonstrate that the canonical model for the packing of dsDNA can be extended to dsRNA viruses.
History
DepositionOct 18, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseJun 12, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / 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
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hy0
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6hy0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0299.png

Downloads & links

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Map

FileDownload / File: emd_0299.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage phi6 nucleocapsid reconstructed with icosahedral symmetry
Voxel sizeX=Y=Z: 1.42 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.22254327 - 0.38795996
Average (Standard dev.)0.0020353894 (±0.017173754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 727.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z727.040727.040727.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.2230.3880.002

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Supplemental data

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Mask #1

Fileemd_0299_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pseudomonas phage phi6

EntireName: Pseudomonas phage phi6 (bacteriophage)
Components
  • Virus: Pseudomonas phage phi6 (bacteriophage)
    • Protein or peptide: Major inner protein P1
    • Protein or peptide: Packaging Enzyme P4
    • Protein or peptide: Major Outer Capsid Protein P8

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Supramolecule #1: Pseudomonas phage phi6

SupramoleculeName: Pseudomonas phage phi6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10879 / Sci species name: Pseudomonas phage phi6 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Pseudomonas syringae (bacteria)
Virus shellShell ID: 1 / Name: Outer Capsid Shell / T number (triangulation number): 13
Virus shellShell ID: 2 / Name: Inner Capsid Shell / T number (triangulation number): 1

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Macromolecule #1: Major inner protein P1

MacromoleculeName: Major inner protein P1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phi6 (bacteriophage)
Molecular weightTheoretical: 85.080711 KDa
SequenceString: MFNLKVKDLN GSARGLTQAF AIGELKNQLS VGALQLPLQF TRTFSASMTS ELLWEVGKGN IDPVMYARLF FQYAQAGGAL SVDELVNQF TEYHQSTACN PEIWRKLTAY ITGSSNRAIK ADAVGKVPPT AILEQLRTLA PSEHELFHHI TTDFVCHVLS P LGFILPDA ...String:
MFNLKVKDLN GSARGLTQAF AIGELKNQLS VGALQLPLQF TRTFSASMTS ELLWEVGKGN IDPVMYARLF FQYAQAGGAL SVDELVNQF TEYHQSTACN PEIWRKLTAY ITGSSNRAIK ADAVGKVPPT AILEQLRTLA PSEHELFHHI TTDFVCHVLS P LGFILPDA AYVYRVGRTA TYPNFYALVD CVRASDLRRM LTALSSVDSK MLQATFKAKG ALAPALISQH LANAATTAFE RS RGNFDAN AVVSSVLTIL GRLWSPSTPK ELDPSARLRN TNGIDQLRSN LALFIAYQDM VKQRGRAEVI FSDEELSSTI IPW FIEAMS EVSPFKLRPI NETTSYIGQT SAIDHMGQPS HVVVYEDWQF AKEITAFTPV KLANNSNQRF LDVEPGISDR MSAT LAPIG NTFAVSAFVK NRTAVYEAVS QRGTVNSNGA EMTLGFPSVV ERDYALDRDP MVAIAALRTG IVDESLEARA SNDLK RSMF NYYAAVMHYA VAHNPEVVVS EHQGVAAEQG SLYLVWNVRT ELRIPVGYNA IEGGSIRTPE PLEAIAYNKP IQPSEV LQA KVLDLANHTT SIHIWPWHEA STEFAYEDAY SVTIRNKRYT AEVKEFELLG LGQRRERVRI LKPTVAHAII QMWYSWF VE DDRTLAAARR TSRDDAEKLA IDGRRMQNAV TLLRKIEMIG TTGIGASAVH LAQSRIVDQM AGRGLIDDSS DLHVGINR H RIRIWAGLAV LQMMGLLSRS EAEALTKVLG DSNALGMVVA TTDIDPSL

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Macromolecule #2: Packaging Enzyme P4

MacromoleculeName: Packaging Enzyme P4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phi6 (bacteriophage)
Molecular weightTheoretical: 35.198426 KDa
SequenceString: MPIVVTQAHI DRVGIAADLL DASPVSLQVL GRPTAINTVV IKTYIAAVME LASKQGGSLA GVDIRPSVLL KDTAIFTKPK AKSADVESD VDVLDTGIYS VPGLARKPVT HRWPSEGIYS GVTALMGATG SGKSITLNEK LRPDVLIRWG EVAEAYDELD T AVHISTLD ...String:
MPIVVTQAHI DRVGIAADLL DASPVSLQVL GRPTAINTVV IKTYIAAVME LASKQGGSLA GVDIRPSVLL KDTAIFTKPK AKSADVESD VDVLDTGIYS VPGLARKPVT HRWPSEGIYS GVTALMGATG SGKSITLNEK LRPDVLIRWG EVAEAYDELD T AVHISTLD EMLIVCIGLG ALGFNVAVDS VRPLLFRLKG AASAGGIVAV FYSLLTDISN LFTQYDCSVV MVVNPMVDAE KI EYVFGQV MASTVGAILC ADGNVSRTMF RTNKGRIFNG AAPLAADTHM PSMDRPTSMK ALDHTSIASV APLERGSVDT DDR NSAPRR GANFSL

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Macromolecule #3: Major Outer Capsid Protein P8

MacromoleculeName: Major Outer Capsid Protein P8 / type: protein_or_peptide / ID: 3 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phi6 (bacteriophage)
Molecular weightTheoretical: 16.018418 KDa
SequenceString:
MLLPVVARAA VPAIESAIAA TPGLVSRIAA AIGSKVSPSA ILAAVKSNPV VAGLTLAQIG STGYDAYQQL LENHPEVAEM LKDLSFKAD EIQPDFIGNL GQYREELELV EDAARFVGGM SNLIRLRQAL ELDIKYYGLK MQLNDMGYRS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
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
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 33.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0.3) / Number images used: 55265
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5muu

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6hy0:
Atomic models of P1, P4 C-terminal fragment and P8 fitted in the bacteriophage phi6 nucleocapsid reconstructed with icosahedral symmetry

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