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- PDB-5kip: Asymmetric unit for the coat proteins of phage Qbeta -

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Basic information

Entry
Database: PDB / ID: 5kip
TitleAsymmetric unit for the coat proteins of phage Qbeta
ComponentsCoat protein
KeywordsVIRUS / Qbeta / ssRNA / phage
Function / homology
Function and homology information


T=3 icosahedral viral capsid / translation repressor activity / structural molecule activity / RNA binding
Similarity search - Function
MS2 Viral Coat Protein / MS2 Viral Coat Protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage Qbeta (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGorzelnik, K.V. / Cui, Z. / Zhang, J.
Funding support United States, 3items
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)GM27099 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ.
Authors: Karl V Gorzelnik / Zhicheng Cui / Catrina A Reed / Joanita Jakana / Ry Young / Junjie Zhang /
Abstract: Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high ...Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qβ, an ssRNA phage specific for the conjugative F-pilus, has a T = 3 icosahedral lattice of coat proteins assembled around its 4,217 nucleotides of genomic RNA (gRNA). In the mature virion, the maturation protein, A, binds to the gRNA and is required for adsorption to the F-pilus. Here, we report the cryo-electron microscopy (cryo-EM) structures of Qβ with and without symmetry applied. The icosahedral structure, at 3.7-Å resolution, resolves loops not previously seen in the published X-ray structure, whereas the asymmetric structure, at 7-Å resolution, reveals A and the gRNA. A contains a bundle of α-helices and replaces one dimer of coat proteins at a twofold axis. The helix bundle binds gRNA, causing denser packing of RNA in its proximity, which asymmetrically expands the surrounding coat protein shell to potentially facilitate RNA release during infection. We observe a fixed pattern of gRNA organization among all viral particles, with the major and minor grooves of RNA helices clearly visible. A single layer of RNA directly contacts every copy of the coat protein, with one-third of the interactions occurring at operator-like RNA hairpins. These RNA-coat interactions stabilize the tertiary structure of gRNA within the virion, which could further provide a roadmap for capsid assembly.
History
DepositionJun 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Database references
Category: citation / em_image_scans ...citation / em_image_scans / em_software / pdbx_audit_support
Item: _citation.journal_id_CSD / _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.3Jul 18, 2018Group: Data collection / Experimental preparation / Category: em_sample_support / Item: _em_sample_support.grid_type
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-8253
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)42,8043
Polymers42,8043
Non-polymers00
Water0
1
A: Coat protein
B: Coat protein
C: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)2,568,253180
Polymers2,568,253180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Coat protein
B: Coat protein
C: Coat protein
x 5


  • icosahedral pentamer
  • 214 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)214,02115
Polymers214,02115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein
B: Coat protein
C: Coat protein
x 6


  • icosahedral 23 hexamer
  • 257 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)256,82518
Polymers256,82518
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Coat protein


Mass: 14268.071 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage Qbeta (virus) / References: UniProt: P03615

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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: bacteriophage Q / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Enterobacteria phage Qbeta (virus)
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
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: Plunged into liquid ethane (FEI VITROBOT MARK III)

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 30000 X
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 10 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2306: / Classification: refinement
EM software
IDNameVersionCategory
1EMANparticle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
5GctfCTF correction
8UCSF Chimeramodel fitting
13RELION1.43D reconstruction
20PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51815 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0082940
ELECTRON MICROSCOPYf_angle_d0.8644026
ELECTRON MICROSCOPYf_dihedral_angle_d6.3882439
ELECTRON MICROSCOPYf_chiral_restr0.053498
ELECTRON MICROSCOPYf_plane_restr0.009534

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