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- PDB-8b3p: CryoEM structure of the round tip (proteins pVII/pVIII/pIX) from ... -

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Basic information

Entry
Database: PDB / ID: 8b3p
TitleCryoEM structure of the round tip (proteins pVII/pVIII/pIX) from the f1 filamentous bacteriophage
Components
  • Capsid protein G8P
  • Tail virion protein G7P
  • Tail virion protein G9P
KeywordsVIRUS / Viral proteins / assembly
Function / homology
Function and homology information


helical viral capsid / host cell membrane / virion component / membrane
Similarity search - Function
Tail virion protein G7P / Tail virion protein G7P / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P
Similarity search - Domain/homology
Tail virion protein G7P / Tail virion protein G9P / Capsid protein G8P
Similarity search - Component
Biological speciesEnterobacteria phage f1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 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
AAA: Tail virion protein G7P
FFF: Tail virion protein G9P
KKK: Capsid protein G8P
PPP: Capsid protein G8P
UUU: Capsid protein G8P
ZZZ: Capsid protein G8P
eee: Capsid protein G8P
jjj: Capsid protein G8P
ooo: Capsid protein G8P
ttt: Capsid protein G8P
yyy: Capsid protein G8P
BBB: Tail virion protein G7P
GGG: Tail virion protein G9P
LLL: Capsid protein G8P
QQQ: Capsid protein G8P
VVV: Capsid protein G8P
aaa: Capsid protein G8P
fff: Capsid protein G8P
kkk: Capsid protein G8P
ppp: Capsid protein G8P
uuu: Capsid protein G8P
222: Capsid protein G8P
CCC: Tail virion protein G7P
HHH: Tail virion protein G9P
MMM: Capsid protein G8P
RRR: Capsid protein G8P
WWW: Capsid protein G8P
bbb: Capsid protein G8P
ggg: Capsid protein G8P
lll: Capsid protein G8P
qqq: Capsid protein G8P
vvv: Capsid protein G8P
111: Capsid protein G8P
DDD: Tail virion protein G7P
III: Tail virion protein G9P
NNN: Capsid protein G8P
SSS: Capsid protein G8P
XXX: Capsid protein G8P
ccc: Capsid protein G8P
hhh: Capsid protein G8P
mmm: Capsid protein G8P
rrr: Capsid protein G8P
www: Capsid protein G8P
zzz: Capsid protein G8P
EEE: Tail virion protein G7P
JJJ: Tail virion protein G9P
OOO: Capsid protein G8P
TTT: Capsid protein G8P
YYY: Capsid protein G8P
ddd: Capsid protein G8P
iii: Capsid protein G8P
nnn: Capsid protein G8P
sss: Capsid protein G8P
xxx: Capsid protein G8P
333: Capsid protein G8P


Theoretical massNumber of molelcules
Total (without water)270,83355
Polymers270,83355
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Tail virion protein G7P / Coat protein C / polypeptide I / Gene 7 protein / G7P


Mass: 3603.215 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage f1 (virus) / Gene: VII / Production host: Escherichia coli (E. coli) / References: UniProt: P69534
#2: Protein/peptide
Tail virion protein G9P / Coat protein C / polypeptide II / G9P


Mass: 3655.270 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage f1 (virus) / Gene: IX / Production host: Escherichia coli (E. coli) / References: UniProt: P69537
#3: Protein/peptide ...
Capsid protein G8P / / Coat protein B / Gene 8 protein / G8P / Major coat protein


Mass: 5212.021 Da / Num. of mol.: 45 / 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

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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
2EPUimage acquisition
4WarpCTF correction
7Cootmodel fitting
9REFMACmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255372 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
RefinementResolution: 2.81→222.442 Å / Cor.coef. Fo:Fc: 0.957 / WRfactor Rwork: 0.289 / SU B: 12.907 / SU ML: 0.226 / Average fsc overall: 0.7375 / Average fsc work: 0.7375 / ESU R: 0.447
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.2885 128336 -
all0.289 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 104.571 Å2
Baniso -1Baniso -2Baniso -3
1-0.127 Å2-0.043 Å20.012 Å2
2--0.194 Å20.065 Å2
3----0.321 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0040.01217930
ELECTRON MICROSCOPYr_angle_refined_deg1.0971.61524185
ELECTRON MICROSCOPYr_dihedral_angle_1_deg3.61852315
ELECTRON MICROSCOPYr_dihedral_angle_2_deg36.70623.529510
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.538153095
ELECTRON MICROSCOPYr_dihedral_angle_4_deg19.1031515
ELECTRON MICROSCOPYr_chiral_restr0.1080.22575
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0212710
ELECTRON MICROSCOPYr_nbd_refined0.2130.213466
ELECTRON MICROSCOPYr_nbtor_refined0.2920.225896
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.2830.270
ELECTRON MICROSCOPYr_mcbond_it4.029.8869425
ELECTRON MICROSCOPYr_mcangle_it7.05714.74411685
ELECTRON MICROSCOPYr_scbond_it6.62910.8668505
ELECTRON MICROSCOPYr_scangle_it10.74715.93312500
ELECTRON MICROSCOPYr_lrange_it17.638185.5568612
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
2.81-2.8831.14594981.14594980.1091.145
2.883-2.9621.02692311.02692310.2061.026
2.962-3.0481.04390461.04390460.3821.043
3.048-3.1420.8587160.8587160.5250.85
3.142-3.2450.66384620.66384620.6870.663
3.245-3.3580.44582020.44582020.8240.445
3.358-3.4850.30579160.30579160.8940.305
3.485-3.6270.26475900.26475900.920.264
3.627-3.7890.24673050.24673050.940.246
3.789-3.9740.23369950.23369950.9540.233
3.974-4.1880.25165960.25165960.9580.251
4.188-4.4420.24963270.24963270.9640.249
4.442-4.7490.26558340.26558340.9630.265
4.749-5.1290.23455110.23455110.9650.234
5.129-5.6190.23650510.23650510.9580.236
5.619-6.2810.24245690.24245690.9470.242
6.281-7.2520.29540170.29540170.9330.295
7.252-8.880.27134110.27134110.9580.271
8.88-12.5480.20726260.20726260.9750.207
12.548-222.4420.28414330.28414330.9840.284

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