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- EMDB-8711: Phage Qbeta in complex with MurA -

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Basic information

Entry
Database: EMDB / ID: EMD-8711
TitlePhage Qbeta in complex with MurA
Map dataEnterobacteria phage Qbeta virion with MurA
Sample
  • Complex: Enterobacteria phage Qbeta virion with MurA
    • Complex: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
      • Protein or peptide: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
    • Virus: Enterobacteria phage Qbeta (virus)
      • Protein or peptide: Maturation protein A2
KeywordsQbeta / ssRNA / phage / virus / VIRUS-TRANSFERASE complex
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 / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / adhesion receptor-mediated virion attachment to host cell / peptidoglycan biosynthetic process / viral release from host cell by cytolysis ...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 / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / adhesion receptor-mediated virion attachment to host cell / peptidoglycan biosynthetic process / viral release from host cell by cytolysis / virion component / cell wall organization / regulation of cell shape / cell cycle / symbiont entry into host cell / cell division / cytoplasm
Similarity search - Function
Assembly protein / Phage maturation protein / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta
Similarity search - Domain/homology
UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Maturation protein A2
Similarity search - Component
Biological speciesEscherichia coli O139:H28 (strain E24377A / ETEC) (bacteria) / Escherichia phage Qbeta (virus) / Enterobacteria phage Qbeta (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.7 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) releaseAug 9, 2017-
Map releaseOct 18, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing 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
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  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5vm7
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5vm7
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8711.png

Downloads & links

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Map

FileDownload / File: emd_8711.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEnterobacteria phage Qbeta virion with MurA
Voxel sizeX=Y=Z: 1.25 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.027086757 - 0.05751116
Average (Standard dev.)0.00084872125 (±0.004180419)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0270.0580.001

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Supplemental data

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Additional map: Enterobacteria phage Qbeta virion with MurA, additional map

Fileemd_8711_additional.map
AnnotationEnterobacteria phage Qbeta virion with MurA, additional 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 : Enterobacteria phage Qbeta virion with MurA

EntireName: Enterobacteria phage Qbeta virion with MurA
Components
  • Complex: Enterobacteria phage Qbeta virion with MurA
    • Complex: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
      • Protein or peptide: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
    • Virus: Enterobacteria phage Qbeta (virus)
      • Protein or peptide: Maturation protein A2

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Supramolecule #1: Enterobacteria phage Qbeta virion with MurA

SupramoleculeName: Enterobacteria phage Qbeta virion with MurA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #3: UDP-N-acetylglucosamine 1-carboxyvinyltransferase

SupramoleculeName: UDP-N-acetylglucosamine 1-carboxyvinyltransferase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)

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Supramolecule #2: Enterobacteria phage Qbeta

SupramoleculeName: Enterobacteria phage Qbeta / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1 / 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: Maturation protein A2

MacromoleculeName: Maturation protein A2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Qbeta (virus)
Molecular weightTheoretical: 48.613078 KDa
SequenceString: 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

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Macromolecule #2: UDP-N-acetylglucosamine 1-carboxyvinyltransferase

MacromoleculeName: UDP-N-acetylglucosamine 1-carboxyvinyltransferase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Source (natural)Organism: Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC
Molecular weightTheoretical: 44.871543 KDa
SequenceString: MDKFRVQGPT KLQGEVTISG AKNAALPILF AALLAEEPVE IQNVPKLKDV DTSMKLLSQL GAKVERNGSV HIDARDVNVF CAPYDLVKT MRASIWALGP LVARFGQGQV SLPGGCTIGA RPVDLHISGL EQLGATIKLE EGYVKASVDG RLKGAHIVMD K VSVGATVT ...String:
MDKFRVQGPT KLQGEVTISG AKNAALPILF AALLAEEPVE IQNVPKLKDV DTSMKLLSQL GAKVERNGSV HIDARDVNVF CAPYDLVKT MRASIWALGP LVARFGQGQV SLPGGCTIGA RPVDLHISGL EQLGATIKLE EGYVKASVDG RLKGAHIVMD K VSVGATVT IMCAATLAEG TTIIENAARE PEIVDTANFL ITLGAKISGQ GTDRIVIEGV ERLGGGVYRV LPDRIETGTF LV AAAISRG KIICRNAQPD TLDAVLAKLR DAGADIEVGE DWISLDMHGK RPKAVNVRTA PHPAFPTDMQ AQFTLLNLVA EGT GFITET VFENRFMHVP ELSRMGAHAE IESNTVICHG VEKLSGAQVM ATDLRASASL VLAGCIAEGT TVVDRIYHID RGYE RIEDK LRALGANIER VKGE

UniProtKB: UDP-N-acetylglucosamine 1-carboxyvinyltransferase

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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

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 30000
Sample stageCooling holder cryogen: NITROGEN
Microscopy ID1
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

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Electron microscopy #1~

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000
Microscopy ID1
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
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8254

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 25597
Image recording ID1

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