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- EMDB-6994: The asymmetric cryo-EM reconstruction of filamentous bacteriophage IKe -

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Basic information

Entry
Database: EMDB / ID: 6994
TitleThe asymmetric cryo-EM reconstruction of filamentous bacteriophage IKe
Map dataThe asymmetric reconstruction of filamentous bacteriophage IKe
SampleFilamentous phageFilamentous bacteriophage:
virus / nucleic-acidNucleic acid
Function / homologyCapsid protein G8P / Bacteriophage M13, G8P, capsid domain superfamily / Phage major coat protein, Gp8 / helical viral capsid / host cell membrane / integral component of membrane / Capsid protein G8P
Function and homology information
SourceFilamentous phage (virus)
Methodhelical reconstruction / cryo EM / 4.5 Å resolution
AuthorsXu JW / Dayan N / Goldbourt A / Xiang Y
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.
Validation ReportPDB-ID: 6a7f

SummaryFull reportAbout validation report
DateDeposition: Jul 3, 2018 / Header (metadata) release: Aug 15, 2018 / Map release: Feb 27, 2019 / Last update: Mar 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6994.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.3 Å/pix.
= 312. Å
240 pix
1.3 Å/pix.
= 312. Å
240 pix
1.3 Å/pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.057654694 - 0.13232106
Average (Standard dev.)0.0005113882 (0.005149029)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin0.00.00.0
Limit239.0239.0239.0
Spacing240240240
CellA=B=C: 312.0 Å
α=β=γ: 90.0 deg.

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
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0580.1320.001

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Supplemental data

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Sample components

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Entire Filamentous phage

EntireName: Filamentous phage / Number of components: 2

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Component #1: virus, Filamentous phage

VirusName: Filamentous phageFilamentous bacteriophage / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Filamentous phage (virus) / Strain: IKe
Source (natural)Host Species: Escherichia coli (E. coli) / Host species strain: A527

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Component #2: nucleic-acid, The asymmetric reconstruction of filamentous bacter...

Nucleic-acidName: The asymmetric reconstruction of filamentous bacteriophage IKe, including major coat protein shell and inner DNA core.
Class: OTHER / Structure: OTHER / Synthetic: No
Sequence:
AEPNAATNYA TEAMDSLKTQ AIDLISQTWP VVTTVVVAGL VIRLFKKFSS KAV
SourceSpecies: Filamentous phage (virus) / Strain: IKe

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 16.77 Å / Delta phi: 38.52 deg.
Sample solutionBuffer solution: 50 mM Tris at pH 7.5, 10 mM MgCl2, 100 mM NaCl
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The asymmetric reconstruction of filamentous bacteriophage IKe. The five equivalent orientation positions are generated after helical reconstruction (EMD-6993). The capsid density subtracted images are performed no sampling 3D classification. The best particle with high likelihood value are used for asymmetric reconstruction, which including outer helical shell and inner DNA core.

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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