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

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Entry
Database: PDB / ID: 6a7f
TitleThe cryo-EM structure of filamentous bacteriophage IKe major coat protein p8 shell assembly.
Componentsmajor coat protein p8
KeywordsVIRAL PROTEIN / filamentous bacteriophage / major coat protein
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
Specimen sourceFilamentous phage (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.4 Å resolution
AuthorsXu, J.W. / Dayan, N. / Goldbourt, A. / Xiang, Y.
Funding supportChina , 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501100China
National Basic Research Program of China(973 Program)2015CB910102China
National Natural Science Foundation of China31470721China
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 Report
SummaryFull reportAbout validation report
DateDeposition: Jul 3, 2018 / Release: Feb 27, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 27, 2019Structure modelrepositoryInitial release
1.1Mar 13, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: major coat protein p8
B: major coat protein p8
C: major coat protein p8
D: major coat protein p8
E: major coat protein p8
F: major coat protein p8
G: major coat protein p8
H: major coat protein p8
I: major coat protein p8
J: major coat protein p8
K: major coat protein p8
L: major coat protein p8
M: major coat protein p8
N: major coat protein p8
O: major coat protein p8
P: major coat protein p8
Q: major coat protein p8
R: major coat protein p8
S: major coat protein p8
T: major coat protein p8
U: major coat protein p8
V: major coat protein p8
W: major coat protein p8
X: major coat protein p8
Y: major coat protein p8
Z: major coat protein p8
a: major coat protein p8
b: major coat protein p8
c: major coat protein p8
d: major coat protein p8


Theoretical massNumber of molelcules
Total (without water)171,01730
Polyers171,01730
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)72430
ΔGint (kcal/M)-769
Surface area (Å2)63380

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Components

#1: Protein/peptide ...
major coat protein p8


Mass: 5700.578 Da / Num. of mol.: 30 / Source: (natural) Filamentous phage (virus) / Strain: IKe / References: UniProt: P03620

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Filamentous phageFilamentous bacteriophage / Type: VIRUS / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Filamentous phage (virus) / Strain: IKe
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Escherichia coli / Strain: A527
Virus shellDiameter: 64 nm
Buffer solutionDetails: 50mM Tris at pH 7.5, 10mM MgCl2, 100mM NaCl / pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4GctfCTF correction
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION2.03D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 38.52 deg. / Axial rise/subunit: 16.77 Å / Axial symmetry: C5
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 112808 / Symmetry type: HELICAL
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL

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