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- PDB-8b3o: CryoEM structure of the pointy tip (proteins pIII/pVI/pVIII) from... -

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Basic information

Entry
Database: PDB / ID: 8b3o
TitleCryoEM structure of the pointy tip (proteins pIII/pVI/pVIII) from the f1 filamentous bacteriophage
Components
  • Attachment protein G3P
  • Capsid protein G8P
  • Head virion protein G6P
KeywordsVIRUS / Viral proteins / Infection
Function / homology
Function and homology information


: / viral extrusion / virion attachment to host cell pilus / adhesion receptor-mediated virion attachment to host cell / helical viral capsid / host cell membrane / virion component / viral capsid / entry receptor-mediated virion attachment to host cell / membrane
Similarity search - Function
Protein of unknown function DUF5455 / Family of unknown function (DUF5455) / Bacteriophage, G3P, N2-domain superfamily / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P
Similarity search - Domain/homology
Attachment protein G3P / Head virion protein G6P / Capsid protein G8P
Similarity search - Component
Biological speciesEnterobacteria phage f1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsConners, R. / McLaren, M. / Gold, V.A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210363/Z/18/Z United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly.
Authors: Rebecca Conners / Rayén Ignacia León-Quezada / Mathew McLaren / Nicholas J Bennett / Bertram Daum / Jasna Rakonjac / Vicki A M Gold /
Abstract: Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular ...Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.
History
DepositionSep 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
KKK: Capsid protein G8P
PPP: Capsid protein G8P
UUU: Capsid protein G8P
ZZZ: Capsid protein G8P
AAA: Head virion protein G6P
FFF: Attachment protein G3P
eee: Capsid protein G8P
jjj: Capsid protein G8P
ooo: Capsid protein G8P
LLL: Capsid protein G8P
QQQ: Capsid protein G8P
VVV: Capsid protein G8P
aaa: Capsid protein G8P
BBB: Head virion protein G6P
GGG: Attachment protein G3P
fff: Capsid protein G8P
kkk: Capsid protein G8P
ppp: Capsid protein G8P
MMM: Capsid protein G8P
RRR: Capsid protein G8P
WWW: Capsid protein G8P
bbb: Capsid protein G8P
CCC: Head virion protein G6P
HHH: Attachment protein G3P
ggg: Capsid protein G8P
lll: Capsid protein G8P
qqq: Capsid protein G8P
NNN: Capsid protein G8P
SSS: Capsid protein G8P
XXX: Capsid protein G8P
ccc: Capsid protein G8P
DDD: Head virion protein G6P
III: Attachment protein G3P
hhh: Capsid protein G8P
mmm: Capsid protein G8P
rrr: Capsid protein G8P
OOO: Capsid protein G8P
TTT: Capsid protein G8P
YYY: Capsid protein G8P
ddd: Capsid protein G8P
EEE: Head virion protein G6P
JJJ: Attachment protein G3P
iii: Capsid protein G8P
nnn: Capsid protein G8P
sss: Capsid protein G8P


Theoretical massNumber of molelcules
Total (without water)457,07945
Polymers457,07945
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area165300 Å2
ΔGint-1893 kcal/mol
Surface area99740 Å2

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Components

#1: Protein/peptide ...
Capsid protein G8P / / Coat protein B / Gene 8 protein / G8P / Major coat protein


Mass: 5212.021 Da / Num. of mol.: 35 / Mutation: Y44M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage f1 (virus) / Gene: VIII / Production host: Escherichia coli (E. coli) / References: UniProt: P69540
#2: Protein
Head virion protein G6P / Coat protein D / G6P


Mass: 12357.984 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage f1 (virus) / Gene: VI / Production host: Escherichia coli (E. coli) / References: UniProt: P69531
#3: Protein
Attachment protein G3P / Gene 3 protein / G3P / Minor coat protein


Mass: 42573.766 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage f1 (virus) / Gene: III / Production host: Escherichia coli (E. coli) / References: UniProt: P69169

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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: Enterobacteria phage f1 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Enterobacteria phage f1 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Escherichia coli / Strain: F+ strains
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Wait time 5 sec., drain time 0 sec., blot force 0, blot time 4 sec.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0253 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk / Date: Jun 20, 2019
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameCategory
4WarpCTF correction
7Cootmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86242 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
RefinementResolution: 2.97→258.782 Å / Cor.coef. Fo:Fc: 0.959 / WRfactor Rwork: 0.3 / SU B: 18.859 / SU ML: 0.313 / Average fsc overall: 0.7467 / Average fsc work: 0.7467 / ESU R: 0.54
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.2996 137443 -
all0.3 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 110.158 Å2
Baniso -1Baniso -2Baniso -3
1-0.727 Å20.05 Å20.018 Å2
2--0.768 Å2-0.035 Å2
3----1.496 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0030.01220860
ELECTRON MICROSCOPYr_angle_refined_deg0.9551.6128145
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.56352675
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.91924.014710
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.663153580
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.4641525
ELECTRON MICROSCOPYr_chiral_restr0.0960.22865
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0214930
ELECTRON MICROSCOPYr_nbd_refined0.2260.213828
ELECTRON MICROSCOPYr_nbtor_refined0.3090.228614
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1230.2326
ELECTRON MICROSCOPYr_mcbond_it1.39911.02110835
ELECTRON MICROSCOPYr_mcangle_it2.62316.49213465
ELECTRON MICROSCOPYr_scbond_it1.17810.98210025
ELECTRON MICROSCOPYr_scangle_it2.19316.42914680
ELECTRON MICROSCOPYr_lrange_it7.472202.13574381
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.97-3.0471.095102071.095102070.1741.095
3.047-3.1311.04999861.04999860.3341.049
3.131-3.2220.88395980.88395980.4840.883
3.222-3.3210.69292650.69292650.6030.692
3.321-3.430.54491820.54491820.7180.544
3.43-3.550.41287770.41287770.7940.412
3.55-3.6840.35484640.35484640.830.354
3.684-3.8340.31681170.31681170.8680.316
3.834-4.0050.30277670.30277670.8950.302
4.005-4.20.29174750.29174750.9210.291
4.2-4.4270.28871570.28871570.9350.288
4.427-4.6960.27266110.27266110.9450.272
4.696-5.020.25264360.25264360.9480.252
5.02-5.4220.23358240.23358240.9460.233
5.422-5.9390.23653700.23653700.9380.236
5.939-6.640.27348810.27348810.9270.273
6.64-7.6660.29643350.29643350.9240.296
7.666-9.3870.25136200.25136200.9520.251
9.387-13.2660.21828240.21828240.9710.218
13.266-258.7820.23815470.23815470.990.238

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