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- PDB-7lhd: The complete model of phage Qbeta virion -

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Basic information

Entry
Database: PDB / ID: 7lhd
TitleThe complete model of phage Qbeta virion
Components
  • Capsid protein
  • Genomic RNA
  • Maturation protein A2
KeywordsVIRUS/RNA / Bacteriophage / Virus / Virion / VIRUS-RNA complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cell wall biogenesis / symbiont-mediated suppression of host peptidoglycan biosynthetic process / viral release via suppression of host peptidoglycan biosynthetic process / virion attachment to host cell pilus / T=3 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / viral release from host cell by cytolysis / translation repressor activity / 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
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Capsid protein / Maturation protein A2
Similarity search - Component
Biological speciesEscherichia virus Qbeta
Escherichia phage Qbeta (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsChang, J.Y. / Zhang, J.
Funding support United States, 4items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Genomic RNA
M: Maturation protein A2
B: Capsid protein
D: Capsid protein
BA: Capsid protein
BB: Capsid protein
BC: Capsid protein
BD: Capsid protein
BE: Capsid protein
BF: Capsid protein
BG: Capsid protein
BH: Capsid protein
BI: Capsid protein
BJ: Capsid protein
BK: Capsid protein
BL: Capsid protein
BM: Capsid protein
BN: Capsid protein
CA: Capsid protein
CB: Capsid protein
CC: Capsid protein
CD: Capsid protein
CE: Capsid protein
CF: Capsid protein
CG: Capsid protein
CH: Capsid protein
CI: Capsid protein
CJ: Capsid protein
CK: Capsid protein
CL: Capsid protein
CM: Capsid protein
CN: Capsid protein
DA: Capsid protein
DB: Capsid protein
DC: Capsid protein
DD: Capsid protein
DE: Capsid protein
DF: Capsid protein
DG: Capsid protein
DH: Capsid protein
DI: Capsid protein
DJ: Capsid protein
DK: Capsid protein
DL: Capsid protein
DM: Capsid protein
DN: Capsid protein
EA: Capsid protein
EB: Capsid protein
EC: Capsid protein
ED: Capsid protein
EE: Capsid protein
EF: Capsid protein
EG: Capsid protein
EH: Capsid protein
EI: Capsid protein
EJ: Capsid protein
EK: Capsid protein
EL: Capsid protein
EM: Capsid protein
EN: Capsid protein
FA: Capsid protein
FB: Capsid protein
FC: Capsid protein
FD: Capsid protein
FE: Capsid protein
FF: Capsid protein
FG: Capsid protein
FH: Capsid protein
FI: Capsid protein
FJ: Capsid protein
FK: Capsid protein
FL: Capsid protein
FM: Capsid protein
FN: Capsid protein
GA: Capsid protein
GB: Capsid protein
GC: Capsid protein
GD: Capsid protein
GE: Capsid protein
GF: Capsid protein
GG: Capsid protein
GH: Capsid protein
GI: Capsid protein
GJ: Capsid protein
GK: Capsid protein
GL: Capsid protein
GM: Capsid protein
GN: Capsid protein
HA: Capsid protein
HB: Capsid protein
HC: Capsid protein
HD: Capsid protein
HE: Capsid protein
HF: Capsid protein
HG: Capsid protein
HH: Capsid protein
HI: Capsid protein
HJ: Capsid protein
HK: Capsid protein
HL: Capsid protein
HM: Capsid protein
HN: Capsid protein
IA: Capsid protein
IB: Capsid protein
IC: Capsid protein
ID: Capsid protein
IE: Capsid protein
IF: Capsid protein
IG: Capsid protein
IH: Capsid protein
II: Capsid protein
IJ: Capsid protein
IK: Capsid protein
IL: Capsid protein
IM: Capsid protein
IN: Capsid protein
JA: Capsid protein
JB: Capsid protein
JC: Capsid protein
JD: Capsid protein
JE: Capsid protein
JF: Capsid protein
JG: Capsid protein
JH: Capsid protein
JI: Capsid protein
JJ: Capsid protein
JK: Capsid protein
JL: Capsid protein
JM: Capsid protein
JN: Capsid protein
KA: Capsid protein
KB: Capsid protein
KC: Capsid protein
KD: Capsid protein
KE: Capsid protein
KF: Capsid protein
KG: Capsid protein
KH: Capsid protein
KI: Capsid protein
KJ: Capsid protein
KK: Capsid protein
KL: Capsid protein
KM: Capsid protein
KN: Capsid protein
LA: Capsid protein
LB: Capsid protein
LC: Capsid protein
LD: Capsid protein
LE: Capsid protein
LF: Capsid protein
LG: Capsid protein
LH: Capsid protein
LI: Capsid protein
LJ: Capsid protein
LK: Capsid protein
LL: Capsid protein
LM: Capsid protein
LN: Capsid protein
MA: Capsid protein
MB: Capsid protein
MC: Capsid protein
MD: Capsid protein
ME: Capsid protein
MF: Capsid protein
MG: Capsid protein
MH: Capsid protein
MI: Capsid protein
MJ: Capsid protein
MK: Capsid protein
ML: Capsid protein
MM: Capsid protein
MN: Capsid protein
NA: Capsid protein
NB: Capsid protein
NC: Capsid protein
ND: Capsid protein
NE: Capsid protein
NF: Capsid protein
NG: Capsid protein
NH: Capsid protein
NI: Capsid protein
NJ: Capsid protein


Theoretical massNumber of molelcules
Total (without water)3,968,882182
Polymers3,968,882182
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain Genomic RNA


Mass: 1352016.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia virus Qbeta / References: GenBank: 668235487
#2: Protein Maturation protein A2 / MP / A2 protein


Mass: 48613.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Qbeta (virus) / References: UniProt: Q8LTE2
#3: Protein ...
Capsid protein / CP / Coat protein


Mass: 14268.071 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Qbeta (virus) / References: UniProt: P03615
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Escherichia virus Qbeta / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia virus Qbeta
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
EM imaging
IDAccelerating voltage (kV)Electron sourceIllumination modeModelModeSpecimen-ID
1300FIELD EMISSION GUNFLOOD BEAMJEOL 3200FSCBRIGHT FIELD1
2200FIELD EMISSION GUNFLOOD BEAMFEI TECNAI F20BRIGHT FIELD1
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1130GATAN K2 SUMMIT (4k x 4k)
2230GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86081 / Symmetry type: POINT

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