+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8709 | |||||||||||||||
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Title | Phage Qbeta with C1 symmetry | |||||||||||||||
Map data | primary map | |||||||||||||||
Sample |
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Keywords | Qbeta / ssRNA / phage / virus | |||||||||||||||
Function / homology | Function and homology information suppression by virus of host cell wall biogenesis / suppression by virus of host peptidoglycan biosynthetic process / viral release via suppression of host peptidoglycan biosynthetic process / virion attachment to host cell pilus / adhesion receptor-mediated virion attachment to host cell / T=3 icosahedral viral capsid / translation repressor activity / viral release from host cell by cytolysis / virion component / structural molecule activity / RNA binding Similarity search - Function | |||||||||||||||
Biological species | Escherichia phage Qbeta (virus) / Enterobacteria phage Qbeta (virus) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||||||||
Authors | Cui Z / Zhang J | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8709.map.gz | 18.9 MB | EMDB map data format | |
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Header (meta data) | emd-8709-v30.xml emd-8709.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
Images | emd_8709.png | 231.6 KB | ||
Filedesc metadata | emd-8709.cif.gz | 5.6 KB | ||
Others | emd_8709_additional.map.gz | 27.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8709 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8709 | HTTPS FTP |
-Validation report
Summary document | emd_8709_validation.pdf.gz | 511.7 KB | Display | EMDB validaton report |
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Full document | emd_8709_full_validation.pdf.gz | 511.3 KB | Display | |
Data in XML | emd_8709_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_8709_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8709 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8709 | HTTPS FTP |
-Related structure data
Related structure data | 5vlzMC 8707C 8708C 8710C 8711C 5vlyC 5vm7C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8709.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.216 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: additional map
File | emd_8709_additional.map | ||||||||||||
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Annotation | additional map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Enterobacteria phage Qbeta
Entire | Name: Enterobacteria phage Qbeta (virus) |
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Components |
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-Supramolecule #1: Enterobacteria phage Qbeta
Supramolecule | Name: 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: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 180 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Qbeta (virus) |
Molecular weight | Theoretical: 14.268071 KDa |
Sequence | String: MAKLETVTLG NIGKDGKQTL VLNPRGVNPT NGVASLSQAG AVPALEKRVT VSVSQPSRNR KNYKVQVKIQ NPTACTANGS CDPSVTRQA YADVTFSFTQ YSTDEERAFV RTELAALLAS PLLIDAIDQL NPAY UniProtKB: Capsid protein |
-Macromolecule #2: Maturation protein A2
Macromolecule | Name: Maturation protein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Qbeta (virus) |
Molecular weight | Theoretical: 48.613078 KDa |
Sequence | String: MPKLPRGLRF GADNEILNDF QELWFPDLFI ESSDTHPWYT LKGRVLNAHL DDRLPNVGGR QVRRTPHRVT VPIASSGLRP VTTVQYDPA ALSFLLNARV DWDFGNGDSA NLVINDFLFR TFAPKEFDFS NSLVPRYTQA FSAFNAKYGT MIGEGLETIK Y LGLLLRRL ...String: MPKLPRGLRF GADNEILNDF QELWFPDLFI ESSDTHPWYT LKGRVLNAHL DDRLPNVGGR QVRRTPHRVT VPIASSGLRP VTTVQYDPA ALSFLLNARV DWDFGNGDSA NLVINDFLFR TFAPKEFDFS NSLVPRYTQA FSAFNAKYGT MIGEGLETIK Y LGLLLRRL REGYRAVKRG DLRALRRVIQ SYHNGKWKPA TAGNLWLEFR YGLMPLFYDI RDVMLDWQNR HDKIQRLLRF SV GHGEDYV VEFDNLYPAV AYFKLKGEIT LERRHRHGIS YANREGYAVF DNGSLRPVSD WKELATAFIN PHEVAWELTP YSF VVDWFL NVGDILAQQG QLYHNIDIVD GFDRRDIRLK SFTIKGERNG RPVNVSASLS AVDLFYSRLH TSNLPFATLD LDTT FSSFK HVLDSIFLLT QRVKR UniProtKB: Maturation protein A2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen 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). |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Image recording | 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 30000 |
Sample stage | Cooling holder cryogen: NITROGEN |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 46471 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |