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- EMDB-23336: Phage Qbeta virion -

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Basic information

Entry
Database: EMDB / ID: EMD-23336
TitlePhage Qbeta virion
Map dataQbeta Virion
Sample
  • Virus: Escherichia virus Qbeta
    • RNA: Genomic RNA
    • Protein or peptide: Maturation protein A2
    • Protein or peptide: Capsid protein
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
Assembly protein / Phage maturation protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid
Similarity search - Domain/homology
Capsid protein / Maturation protein A2
Similarity search - Component
Biological speciesEscherichia virus Qbeta / Bacteriophage Q-beta (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsChang JY / Zhang J
Funding support United States, 4 items
OrganizationGrant numberCountry
Welch FoundationA-1863 United States
National Science Foundation (NSF, United States)MCB-1902392 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI137696 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI095208 United States
CitationJournal: Viruses / Year: 2022
Title: Structural Assembly of Qβ Virion and Its Diverse Forms of Virus-like Particles.
Authors: Jeng-Yih Chang / Karl V Gorzelnik / Jirapat Thongchol / Junjie Zhang /
Abstract: The coat proteins (CPs) of single-stranded RNA bacteriophages (ssRNA phages) directly assemble around the genomic RNA (gRNA) to form a near-icosahedral capsid with a single maturation protein (Mat) ...The coat proteins (CPs) of single-stranded RNA bacteriophages (ssRNA phages) directly assemble around the genomic RNA (gRNA) to form a near-icosahedral capsid with a single maturation protein (Mat) that binds the gRNA and interacts with the retractile pilus during infection of the host. Understanding the assembly of ssRNA phages is essential for their use in biotechnology, such as RNA protection and delivery. Here, we present the complete gRNA model of the ssRNA phage Qβ, revealing that the 3' untranslated region binds to the Mat and the 4127 nucleotides fold domain-by-domain, and is connected through long-range RNA-RNA interactions, such as kissing loops. Thirty-three operator-like RNA stem-loops are located and primarily interact with the asymmetric A/B CP-dimers, suggesting a pathway for the assembly of the virions. Additionally, we have discovered various forms of the virus-like particles (VLPs), including the canonical = 3 icosahedral, larger = 4 icosahedral, prolate, oblate forms, and a small prolate form elongated along the 3-fold axis. These particles are all produced during a normal infection, as well as when overexpressing the CPs. When overexpressing the shorter RNA fragments encoding only the CPs, we observed an increased percentage of the smaller VLPs, which may be sufficient to encapsidate a shorter RNA.
History
DepositionJan 22, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateMar 9, 2022-
Current statusMar 9, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lhd
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23336.png

Downloads & links

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Map

FileDownload / File: emd_23336.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationQbeta Virion
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: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.04093264 - 0.07908933
Average (Standard dev.)0.0013869614 (±0.0056403447)
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-0.0410.0790.001

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Supplemental data

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Additional map: Unsharpened Map

Fileemd_23336_additional_1.map
AnnotationUnsharpened 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 : Escherichia virus Qbeta

EntireName: Escherichia virus Qbeta
Components
  • Virus: Escherichia virus Qbeta
    • RNA: Genomic RNA
    • Protein or peptide: Maturation protein A2
    • Protein or peptide: Capsid protein

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Supramolecule #1: Escherichia virus Qbeta

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

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Macromolecule #1: Genomic RNA

MacromoleculeName: Genomic RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Escherichia virus Qbeta
Molecular weightTheoretical: 1.3520166249999999 MDa
SequenceString: GGGGACCCCC UUUAGGGGGU CACCUCACAC AGCAGUACUU CACUGAGUAU AAGAGGACAU AUGCCUAAAU UACCGCGUGG UCUGCGUUU CGGAGCCGAU AAUGAAAUUC UUAAUGAUUU UCAGGAGCUC UGGUUUCCAG ACCUCUUUAU CGAAUCUUCC G ACACGCAU ...String:
GGGGACCCCC UUUAGGGGGU CACCUCACAC AGCAGUACUU CACUGAGUAU AAGAGGACAU AUGCCUAAAU UACCGCGUGG UCUGCGUUU CGGAGCCGAU AAUGAAAUUC UUAAUGAUUU UCAGGAGCUC UGGUUUCCAG ACCUCUUUAU CGAAUCUUCC G ACACGCAU CCGUGGUACA CACUGAAGGG UCGUGUGUUG AACGCCCACC UUGAUGAUCG UCUACCUAAU GUAGGCGGUC GC CAGGUAA GGCGCACUCC ACAUCGCGUC ACCGUUCCGA UUGCCUCUUC AGGCCUUCGU CCGGUAACAA CCGUUCAGUA UGA UCCCGC AGCACUAUCG UUCUUAUUGA ACGCUCGUGU UGACUGGGAU UUCGGUAAUG GCGAUAGUGC GAACCUUGUC AUUA AUGAC UUUCUGUUUC GCACCUUUGC ACCUAAGGAG UUUGAUUUUU CGAACUCCUU AGUUCCUCGU UAUACUCAGG CCUUC UCCG CGUUUAAUGC CAAGUAUGGC ACUAUGAUCG GCGAAGGGCU CGAGACUAUA AAAUAUCUCG GGCUUUUACU GCGCAG ACU GCGUGAGGGU UACCGCGCUG UUAAGCGUGG CGAUUUACGU GCUCUUCGUA GGGUUAUCCA GUCCUACCAU AAUGGUA AG UGGAAACCGG CUACUGCUGG UAAUCUCUGG CUUGAAUUUC GUUAUGGCCU UAUGCCUCUC UUUUAUGACA UCAGAGAU G UCAUGUUAGA CUGGCAGAAC CGUCAUGAUA AGAUUCAACG CCUCCUUCGG UUUUCUGUUG GUCACGGCGA GGAUUACGU UGUCGAAUUC GACAAUCUGU ACCCUGCCGU UGCUUACUUU AAACUGAAAG GGGAGAUUAC ACUCGAACGC CGUCAUCGUC AUGGCAUAU CUUACGCUAA CCGCGAAGGA UAUGCUGUUU UCGACAACGG UUCCCUUCGG CCUGUGUCCG AUUGGAAGGA G CUUGCCAC UGCAUUCAUC AAUCCGCAUG AAGUUGCUUG GGAGUUAACU CCCUACAGCU UCGUUGUUGA UUGGUUCUUG AA UGUUGGU GACAUACUUG CUCAACAAGG UCAGCUAUAU CAUAAUAUCG AUAUUGUAGA CGGCUUUGAC AGACGUGACA UCC GGCUCA AAUCUUUCAC CAUAAAAGGU GAACGAAAUG GGCGGCCUGU UAACGUUUCU GCUAGCCUGU CUGCUGUCGA UUUA UUUUA CAGCCGACUC CAUACGAGCA AUCUUCCGUU CGCUACACUA GAUCUUGAUA CCACCUUUAG UUCGUUUAAA CACGU UCUU GAUAGUAUCU UUUUAUUAAC CCAACGCGUA AAGCGUUGAA ACUUUGGGUC AAUUUGAUCA UGGCAAAAUU AGAGAC UGU UACUUUAGGU AACAUCGGGA AAGAUGGAAA ACAAACUCUG GUCCUCAAUC CGCGUGGGGU AAAUCCCACU AACGGCG UU GCCUCGCUUU CACAAGCGGG UGCAGUUCCU GCGCUGGAGA AGCGUGUUAC CGUUUCGGUA UCUCAGCCUU CUCGCAAU C GUAAGAACUA CAAGGUCCAG GUUAAGAUCC AGAACCCGAC CGCUUGCACU GCAAACGGUU CUUGUGACCC AUCCGUUAC UCGCCAGGCA UAUGCUGACG UGACCUUUUC GUUCACGCAG UAUAGUACCG AUGAGGAACG AGCUUUUGUU CGUACAGAGC UUGCUGCUC UGCUCGCUAG UCCUCUGCUG AUCGAUGCUA UUGAUCAGCU GAACCCAGCG UAUUGAACAC UGCUCAUUGC C GGUGGUGG CUCAGGGUCA AAACCCGAUC CGGUUAUUCC GGAUCCACCG AUUGAUCCGC CGCCAGGGAC AGGUAAGUAU AC CUGUCCC UUCGCAAUUU GGUCCCUAGA GGAGGUUUAC GAGCCUCCUA CUAAGAACCG ACCGUGGCCU AUCUAUAAUG CUG UUGAAC UCCAGCCUCG CGAAUUUGAU GUUGCCCUCA AAGAUCUUUU GGGCAAUACA AAGUGGCGUG AUUGGGAUUC UCGG CUUAG UUAUACCACG UUCCGCGGUU GCCGUGGCAA UGGUUAUAUU GACCUUGAUG CGACUUAUCU UGCUACUGAU CAGGC UAUG CGUGAUCAGA AGUAUGAUAU UCGCGAGGGC AAGAAACCUG GUGCUUUCGG UAACAUUGAG CGAUUCAUUU AUCUUA AGU CGAUAAAUGC UUAUUGCUCU CUUAGCGAUA UUGCGGCCUA UCACGCCGAU GGCGUGAUAG UUGGCUUUUG GCGCGAU CC AUCCAGCGGU GGUGCCAUAC CGUUUGACUU CACUAAGUUU GAUAAGACUA AAUGUCCUAU UCAAGCCGUG AUAGUCGU U CCUCGUGCUU AGUAACUAAG GAUGAAAUGC AUGUCUAAGA CAGCAUCUUC GCGUAACUCU CUCAGCGCAC AAUUGCGCC GAGCCGCGAA CACAAGAAUU GAGGUUGAAG GUAACCUCGC ACUUUCCAUU GCCAACGAUU UACUGUUGGC CUAUGGUCAG UCGCCAUUU AACUCUGAGG CUGAGUGUAU UUCAUUCAGC CCGAGAUUCG ACGGGACCCC GGAUGACUUU AGGAUAAAUU A UCUUAAAG CCGAGAUCAU GUCGAAGUAU GACGACUUCA GCCUAGGUAU UGAUACCGAA GCUGUUGCCU GGGAGAAGUU CC UGGCAGC AGAGGCUGAA UGUGCUUUAA CGAACGCUCG UCUCUAUAGG CCUGACUACA GUGAGGAUUU CAAUUUCUCA CUG GGCGAG UCAUGUAUAC ACAUGGCUCG UAGAAAAAUA GCCAAGCUAA UAGGAGAUGU UCCGUCCGUU GAGGGUAUGU UGCG UCACU GCCGAUUUUC UGGCGGUGCU ACAACAACGA AUAACCGUUC GUACGGUCAU CCGUCCUUCA AGUUUGCGCU UCCGC AAGC GUGUACGCCU CGGGCUUUGA AGUAUGUUUU AGCUCUCAGA GCUUCUACAC AUUUCGAUAU CAGAAUUUCU GAUAUU AGC CCUUUUAAUA AAGCAGUUAC UGUACCUAAG AACAGUAAGA CAGAUCGUUG UAUUGCUAUC GAACCUGGUU GGAAUAU GU UUUUCCAACU GGGUAUCGGU GGCAUUCUAC GCGAUCGGUU GCGUUGCUGG GGUAUCGAUC UGAAUGAUCA GACGAUAA A UCAGCGCCGC GCUCACGAAG GCUCCGUUAC UAAUAACUUA GCAACGGUUG AUCUCUCAGC GGCAAGCGAU UCUAUAUCU CUUGCCCUCU GUGAGCUCUU AUUGCCCCCA GGCUGGUUUG AGGUUCUUAU GGACCUCAGA UCACCUAAGG GGCGAUUGCC UGACGGUAG UGUUGUUACC UACGAGAAGA UUUCUUCUAU GGGUAACGGU UACACAUUCG AGCUCGAGUC GCUUAUUUUU G CUUCUCUC GCUCGUUCCG UUUGUGAGAU ACUGGACUUA GACUCGUCUG AGGUCACUGU UUACGGAGAC GAUAUUAUUU UA CCGUCCU GUGCAGUCCC UGCCCUCCGG GAAGUUUUUA AGUAUGUUGG UUUUACGACC AAUACUAAAA AGACUUUUUC CGA GGGGCC GUUCAGAGAG UCGUGCGGCA AGCACUACUA UUCUGGCGUA GAUGUUACUC CCUUUUACAU ACGUCACCGU AUAG UGAGU CCUGCCGAUU UAAUACUGGU UUUGAAUAAC CUAUAUCGGU GGGCCACAAU UGACGGCGUA UGGGAUCCUA GGGCC CAUU CUGUGUACCU CAAGUAUCGU AAGUUGCUGC CUAAACAGCU GCAACGUAAU ACUAUACCUG AUGGUUACGG UGAUGG UGC CCUCGUCGGA UCGGUCCUAA UCAAUCCUUU CGCGAAAAAC CGCGGGUGGA UCCGGUACGU ACCGGUGAUU ACGGACC AU ACAAGGGACC GAGAGCGCGC UGAGUUGGGG UCGUAUCUCU ACGACCUCUU CUCGCGUUGU CUCUCGGAAA GUAACGAU G GGUUGCCUCU UAGGGGUCCA UCGGGUUGCG AUUCUGCGGA UCUAUUUGCC AUCGAUCAGC UUAUCUGUAG GAGUAAUCC UACGAAGAUA AGCAGGUCUA CCGGCAAAUU CGAUAUACAG UAUAUCGCGU GCAGUAGCCG UGUUCUGGCA CCCUACGGGG UCUUCCAGG GCACGAAGGU UGCGUCUCUA CACGAGGCGU AACCUGGGAG GGCGCCAAUA UGGCGCCUAA UUGUGAAUAA A UUAUCACA AUUACUCUUA CGAGUGAGAG GGGGAUCUGC UUUGCCCUCU CUCCUCCCA

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Macromolecule #2: Maturation protein A2

MacromoleculeName: Maturation protein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteriophage Q-beta (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

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Macromolecule #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 180 / Enantiomer: LEVO
Source (natural)Organism: Bacteriophage Q-beta (virus)
Molecular weightTheoretical: 14.268071 KDa
SequenceString:
MAKLETVTLG NIGKDGKQTL VLNPRGVNPT NGVASLSQAG AVPALEKRVT VSVSQPSRNR KNYKVQVKIQ NPTACTANGS CDPSVTRQA YADVTFSFTQ YSTDEERAFV RTELAALLAS PLLIDAIDQL NPAY

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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
VitrificationCryogen name: ETHANE

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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) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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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) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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:

8709

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86081
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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