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- PDB-7wmp: Tail structure of Helicobacter pylori bacteriophage KHP30 -

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Basic information

Entry
Database: PDB / ID: 7wmp
TitleTail structure of Helicobacter pylori bacteriophage KHP30
Components
  • Adaptor protein gp12
  • Nozzle protein gp25
  • Portal protein
KeywordsVIRAL PROTEIN / PHAGE / PHAGE TAIL / CRYOEM / VIRUS
Function / homologysymbiont genome ejection through host cell envelope, short tail mechanism / viral capsid / Uncharacterized protein / Phage protein / Portal protein
Function and homology information
Biological speciesHelicobacter phage KHP30 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKamiya, R. / Uchiyama, J. / Matsuzaki, S. / Murata, K. / Iwasaki, K. / Miyazaki, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K18521 Japan
Japan Society for the Promotion of Science (JSPS)18K06154 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of Helicobacter pylori bacteriophage KHP30
Authors: Kamiya, R. / Uchiyama, J. / Matsuzaki, S. / Murata, K. / Iwasaki, K. / Miyazaki, N.
History
DepositionJan 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
a: Portal protein
b: Portal protein
c: Portal protein
d: Portal protein
e: Portal protein
f: Portal protein
g: Portal protein
h: Portal protein
i: Portal protein
j: Portal protein
k: Portal protein
l: Portal protein
m: Adaptor protein gp12
n: Adaptor protein gp12
o: Adaptor protein gp12
p: Adaptor protein gp12
q: Adaptor protein gp12
r: Adaptor protein gp12
s: Adaptor protein gp12
t: Adaptor protein gp12
u: Adaptor protein gp12
v: Adaptor protein gp12
w: Adaptor protein gp12
x: Adaptor protein gp12
A: Nozzle protein gp25
B: Nozzle protein gp25
C: Nozzle protein gp25
D: Nozzle protein gp25
E: Nozzle protein gp25
F: Nozzle protein gp25
G: Nozzle protein gp25
H: Nozzle protein gp25
I: Nozzle protein gp25
J: Nozzle protein gp25
K: Nozzle protein gp25
L: Nozzle protein gp25


Theoretical massNumber of molelcules
Total (without water)1,463,83036
Polymers1,463,83036
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Portal protein / Head-to-tail connector gp8 / Putative portal protein ORF17


Mass: 69634.734 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Helicobacter phage KHP30 (virus) / References: UniProt: I7HHN4
#2: Protein
Adaptor protein gp12


Mass: 22609.309 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Helicobacter phage KHP30 (virus) / References: UniProt: I7HHN3
#3: Protein
Nozzle protein gp25


Mass: 29741.775 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Helicobacter phage KHP30 (virus) / References: UniProt: I7HFX1

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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: Helicobacter phage KHP / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Helicobacter phage KHP (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Virus shellName: Head / Diameter: 700 nm / Triangulation number (T number): 9
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 50 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 32655
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27422 / Symmetry type: POINT

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