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- EMDB-6993: The cryo-EM structure of filamentous bacteriophage IKe applied wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-6993
TitleThe cryo-EM structure of filamentous bacteriophage IKe applied with C5 and helical parameters.
Map dataThe cryo-EM structure of filamentous bacteriophage IKe applied with helical parameters and 5-fold symmetry.
Sample
  • Virus: Filamentous phage (virus)
    • Protein or peptide: major coat protein p8
Keywordsfilamentous bacteriophage / major coat protein / VIRAL PROTEIN
Function / homologyPhage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / helical viral capsid / host cell membrane / membrane / Capsid protein G8P
Function and homology information
Biological speciesFilamentous phage (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsXu JW / Dayan N
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501100 China
National Basic Research Program of China (973 Program)2015CB910102 China
National Natural Science Foundation of China31470721 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Cryo-electron microscopy structure of the filamentous bacteriophage IKe.
Authors: Jingwei Xu / Nir Dayan / Amir Goldbourt / Ye Xiang /
Abstract: The filamentous bacteriophage IKe infects cells bearing IncN pili. We report the cryo-electron microscopy structure of the micrometer-long IKe viral particle at a resolution of 3.4 Å. The major ...The filamentous bacteriophage IKe infects cells bearing IncN pili. We report the cryo-electron microscopy structure of the micrometer-long IKe viral particle at a resolution of 3.4 Å. The major coat protein [protein 8 (p8)] consists of 47 residues that fold into a ∼68-Å-long helix. An atomic model of the coat protein was built. Five p8 helices in a horizontal layer form a pentamer, and symmetrically neighboring p8 layers form a right-handed helical cylinder having a rise per pentamer of 16.77 Å and a twist of 38.52°. The inner surface of the capsid cylinder is positively charged and has direct interactions with the encapsulated circular single-stranded DNA genome, which has an electron density consistent with an unusual left-handed helix structure. Similar to capsid structures of other filamentous viruses, strong capsid packing in the IKe particle is maintained by hydrophobic residues. Despite having a different length and large sequence differences from other filamentous phages, π-π interactions were found between Tyr9 of one p8 and Trp29 of a neighboring p8 in IKe that are similar to interactions observed in phage M13, suggesting that, despite sequence divergence, overall structural features are maintained.
History
DepositionJul 3, 2018-
Header (metadata) releaseAug 8, 2018-
Map releaseFeb 27, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.044
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.044
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6a7f
  • Surface level: 0.044
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6a7f
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6993.png

Downloads & links

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Map

FileDownload / File: emd_6993.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-EM structure of filamentous bacteriophage IKe applied with helical parameters and 5-fold symmetry.
Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.044 / Movie #1: 0.044
Minimum - Maximum-0.105677254 - 0.27732947
Average (Standard dev.)0.0004895081 (±0.0073515475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1060.2770.000

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Supplemental data

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Sample components

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Entire : Filamentous phage

EntireName: Filamentous phage (virus)
Components
  • Virus: Filamentous phage (virus)
    • Protein or peptide: major coat protein p8

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Supramolecule #1: Filamentous phage

SupramoleculeName: Filamentous phage / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12420 / Sci species name: Filamentous phage / Sci species strain: IKe / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli) / Strain: A527
Virus shellShell ID: 1 / Diameter: 64.0 Å

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Macromolecule #1: major coat protein p8

MacromoleculeName: major coat protein p8 / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Filamentous phage (virus) / Strain: IKe
Molecular weightTheoretical: 5.700578 KDa
SequenceString:
AEPNAATNYA TEAMDSLKTQ AIDLISQTWP VVTTVVVAGL VIRLFKKFSS KAV

UniProtKB: Capsid protein G8P

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5 / Details: 50mM Tris at pH 7.5, 10mM MgCl2, 100mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2hi5

Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2)
Final reconstructionApplied symmetry - Helical parameters - Δz: 16.77 Å
Applied symmetry - Helical parameters - Δ&Phi: 38.52 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 112808

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6a7f:
The cryo-EM structure of filamentous bacteriophage IKe major coat protein p8 shell assembly.

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