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- EMDB-8253: Phage Qbeta with icosahedral symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-8253
TitlePhage Qbeta with icosahedral symmetry
Map dataIcosahedral reconstruction of phage Qbeta
Samplebacteriophage Q != Enterobacteria phage Qbeta

bacteriophage Q

  • Virus: Enterobacteria phage Qbeta (virus)
    • Protein or peptide: Coat protein
KeywordsQbeta / ssRNA / phage / virus
Function / homologyLevivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / T=3 icosahedral viral capsid / translation repressor activity / structural molecule activity / RNA binding / Capsid protein
Function and homology information
Biological speciesEnterobacteria phage Qbeta (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGorzelnik KV / Cui Z / Zhang J
Funding support United States, 3 items
OrganizationGrant numberCountry
Welch FoundationA-1863 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM27099 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ.
Authors: Karl V Gorzelnik / Zhicheng Cui / Catrina A Reed / Joanita Jakana / Ry Young / Junjie Zhang /
Abstract: Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high ...Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qβ, an ssRNA phage specific for the conjugative F-pilus, has a T = 3 icosahedral lattice of coat proteins assembled around its 4,217 nucleotides of genomic RNA (gRNA). In the mature virion, the maturation protein, A, binds to the gRNA and is required for adsorption to the F-pilus. Here, we report the cryo-electron microscopy (cryo-EM) structures of Qβ with and without symmetry applied. The icosahedral structure, at 3.7-Å resolution, resolves loops not previously seen in the published X-ray structure, whereas the asymmetric structure, at 7-Å resolution, reveals A and the gRNA. A contains a bundle of α-helices and replaces one dimer of coat proteins at a twofold axis. The helix bundle binds gRNA, causing denser packing of RNA in its proximity, which asymmetrically expands the surrounding coat protein shell to potentially facilitate RNA release during infection. We observe a fixed pattern of gRNA organization among all viral particles, with the major and minor grooves of RNA helices clearly visible. A single layer of RNA directly contacts every copy of the coat protein, with one-third of the interactions occurring at operator-like RNA hairpins. These RNA-coat interactions stabilize the tertiary structure of gRNA within the virion, which could further provide a roadmap for capsid assembly.
History
DepositionJun 16, 2016-
Header (metadata) releaseJul 20, 2016-
Map releaseOct 5, 2016-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5kip
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5kip
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8253.png

Downloads & links

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Map

FileDownload / File: emd_8253.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral reconstruction of phage Qbeta
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 320 pix.
= 384. Å		1.2 Å/pix.
x 320 pix.
= 384. Å		1.2 Å/pix.
x 320 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.06420996 - 0.0819913
Average (Standard dev.)0.00034809398 (±0.0046583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z384.000384.000384.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0640.0820.000

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Supplemental data

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Sample components

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Entire : bacteriophage Q

EntireName: bacteriophage Q
Components
  • Virus: Enterobacteria phage Qbeta (virus)
    • Protein or peptide: Coat protein

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Supramolecule #1: Enterobacteria phage Qbeta

SupramoleculeName: Enterobacteria phage Qbeta / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 39803 / Sci species name: Enterobacteria phage Qbeta / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage Qbeta (virus)
Molecular weightTheoretical: 14.268071 KDa
SequenceString:
MAKLETVTLG NIGKDGKQTL VLNPRGVNPT NGVASLSQAG AVPALEKRVT VSVSQPSRNR KNYKVQVKIQ NPTACTANGS CDPSVTRQA YADVTFSFTQ YSTDEERAFV RTELAALLAS PLLIDAIDQL NPAY

UniProtKB: Capsid protein

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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
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III
Details: Plunged into liquid ethane (FEI VITROBOT MARK III).

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Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 30000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: OTHER / Details: EMAN2 generated the initial model.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 51815
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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