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- EMDB-8710: A2 with sequestered coat dimer protein and interacting RNAs -

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Basic information

Entry
Database: EMDB / ID: EMD-8710
TitleA2 with sequestered coat dimer protein and interacting RNAs
Map dataA2 with internalized coat protein dimer
Sample
  • Virus: Enterobacteria phage Qbeta (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: 6.25 Å
AuthorsCui Z / Zhang J
Funding support United States, 4 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)U24GM116787 United States
Public Health ServiceGM27099 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structures of Qβ virions, virus-like particles, and the Qβ-MurA complex reveal internal coat proteins and the mechanism of host lysis.
Authors: Zhicheng Cui / Karl V Gorzelnik / Jeng-Yih Chang / Carrie Langlais / Joanita Jakana / Ry Young / Junjie Zhang /
Abstract: In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the ...In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the canonical Qβ the maturation protein, A, has an additional role as the lysis protein, by its ability to bind and inhibit MurA, which is involved in peptidoglycan biosynthesis. Here, we determined structures of Qβ virions, virus-like particles, and the Qβ-MurA complex using single-particle cryoelectron microscopy, at 4.7-Å, 3.3-Å, and 6.1-Å resolutions, respectively. We identified the outer surface of the β-region in A as the MurA-binding interface. Moreover, the pattern of MurA mutations that block Qβ lysis and the conformational changes of MurA that facilitate A binding were found to be due to the intimate fit between A and the region encompassing the closed catalytic cleft of substrate-liganded MurA. Additionally, by comparing the Qβ virion with Qβ virus-like particles that lack a maturation protein, we observed a structural rearrangement in the capsid coat proteins that is required to package the viral gRNA in its dominant conformation. Unexpectedly, we found a coat protein dimer sequestered in the interior of the virion. This coat protein dimer binds to the gRNA and interacts with the buried α-region of A, suggesting that it is sequestered during the early stage of capsid formation to promote the gRNA condensation required for genome packaging. These internalized coat proteins are the most asymmetrically arranged major capsid proteins yet observed in virus structures.
History
DepositionApr 26, 2017-
Header (metadata) releaseMay 17, 2017-
Map releaseOct 18, 2017-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8710.png

Downloads & links

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Map

FileDownload / File: emd_8710.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA2 with internalized coat protein dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 320 pix.
= 400. Å		1.25 Å/pix.
x 320 pix.
= 400. Å		1.25 Å/pix.
x 320 pix.
= 400. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.035975836 - 0.06313045
Average (Standard dev.)0.000020653793 (±0.0007346541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.251.251.25
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z400.000400.000400.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ288288288
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0360.0630.000

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Supplemental data

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Sample components

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Entire : Enterobacteria phage Qbeta

EntireName: Enterobacteria phage Qbeta (virus)
Components
  • Virus: Enterobacteria phage Qbeta (virus)

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Supramolecule #1: Enterobacteria phage Qbeta

SupramoleculeName: Enterobacteria phage Qbeta / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / 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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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: Blotted for 6s, Plunged into liquid ethane (FEI VITROBOT MARK III).

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Electron microscopy #1

Microscopy ID1
MicroscopeJEOL 3200FSC
Image recordingImage recording ID: 1 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 0.2 sec. / Average electron dose: 1.0 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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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TECNAI F20
Image recordingImage recording ID: 2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 0.2 sec. / Average electron dose: 1.1 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 29000
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: EMDB MAP
EMDB ID:

8254

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 47621
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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