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- PDB-7f2p: The head structure of Helicobacter pylori bacteriophage KHP40 -

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Basic information

Entry
Database: PDB / ID: 7f2p
TitleThe head structure of Helicobacter pylori bacteriophage KHP40
Components
  • Cement protein gp16
  • KHP40 MCP
KeywordsVIRUS / CAPSID / PHAGE / PHAGE HEAD / CRYOEM
Function / homologyProtein of unknown function DUF4043 / Phage capsid protein / Uncharacterized protein / DUF4043 family protein
Function and homology information
Biological speciesHelicobacter phage KHP40 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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: Structure / Year: 2022
Title: Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy.
Authors: Ryosuke Kamiya / Jumpei Uchiyama / Shigenobu Matsuzaki / Kazuyoshi Murata / Kenji Iwasaki / Naoyuki Miyazaki /
Abstract: The acid-stable capsid structures of Helicobacter pylori phages KHP30 and KHP40 are solved at 2.7 and 3.0 Å resolutions by cryoelectron microscopy, respectively. The capsids have icosahedral T = 9 ...The acid-stable capsid structures of Helicobacter pylori phages KHP30 and KHP40 are solved at 2.7 and 3.0 Å resolutions by cryoelectron microscopy, respectively. The capsids have icosahedral T = 9 symmetry and consist of each 540 copies of 2 structural proteins, a major capsid protein, and a cement protein. The major capsid proteins form 12 pentagonal capsomeres occupying icosahedral vertexes and 80 hexagonal capsomeres located at icosahedral faces and edges. The major capsid protein has a unique protruding loop extending to the neighboring subunit that stabilizes hexagonal capsomeres. Furthermore, the capsid is decorated with trimeric cement proteins with a jelly roll motif. The cement protein trimer sits on the quasi-three-fold axis formed by three major capsid protein capsomeres, thereby enhancing the particle stability by connecting these capsomeres. Sequence and structure comparisons between the related Helicobacter pylori phages suggest a possible mechanism of phage adaptation to the human gastric environment.
History
DepositionJun 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.year / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.2Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Jul 2, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-30800
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  • Superimposition on EM map
  • EMDB-30800
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Cement protein gp16
2: Cement protein gp16
3: Cement protein gp16
4: Cement protein gp16
5: Cement protein gp16
6: Cement protein gp16
7: Cement protein gp16
8: Cement protein gp16
9: Cement protein gp16
a: KHP40 MCP
b: KHP40 MCP
c: KHP40 MCP
d: KHP40 MCP
e: KHP40 MCP
f: KHP40 MCP
g: KHP40 MCP
h: KHP40 MCP
i: KHP40 MCP


Theoretical massNumber of molelcules
Total (without water)506,92318
Polymers506,92318
Non-polymers00
Water00
1
1: Cement protein gp16
2: Cement protein gp16
3: Cement protein gp16
4: Cement protein gp16
5: Cement protein gp16
6: Cement protein gp16
7: Cement protein gp16
8: Cement protein gp16
9: Cement protein gp16
a: KHP40 MCP
b: KHP40 MCP
c: KHP40 MCP
d: KHP40 MCP
e: KHP40 MCP
f: KHP40 MCP
g: KHP40 MCP
h: KHP40 MCP
i: KHP40 MCP
x 60


Theoretical massNumber of molelcules
Total (without water)30,415,4071080
Polymers30,415,4071080
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: Cement protein gp16
2: Cement protein gp16
3: Cement protein gp16
4: Cement protein gp16
5: Cement protein gp16
6: Cement protein gp16
7: Cement protein gp16
8: Cement protein gp16
9: Cement protein gp16
a: KHP40 MCP
b: KHP40 MCP
c: KHP40 MCP
d: KHP40 MCP
e: KHP40 MCP
f: KHP40 MCP
g: KHP40 MCP
h: KHP40 MCP
i: KHP40 MCP
x 5


  • icosahedral pentamer
  • 2.53 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)2,534,61790
Polymers2,534,61790
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Cement protein gp16
2: Cement protein gp16
3: Cement protein gp16
4: Cement protein gp16
5: Cement protein gp16
6: Cement protein gp16
7: Cement protein gp16
8: Cement protein gp16
9: Cement protein gp16
a: KHP40 MCP
b: KHP40 MCP
c: KHP40 MCP
d: KHP40 MCP
e: KHP40 MCP
f: KHP40 MCP
g: KHP40 MCP
h: KHP40 MCP
i: KHP40 MCP
x 6


  • icosahedral 23 hexamer
  • 3.04 MDa, 108 polymers
Theoretical massNumber of molelcules
Total (without water)3,041,541108
Polymers3,041,541108
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Cement protein gp16


Mass: 13469.469 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Helicobacter phage KHP40 (virus) / References: UniProt: I7GUT5
#2: Protein
KHP40 MCP


Mass: 42855.359 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Helicobacter phage KHP40 (virus) / References: UniProt: I7HFY0
Has protein modificationN

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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 KHP40 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Helicobacter phage KHP40 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
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: 298 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
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
8PHENIXmodel refinement
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6772 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00734710
ELECTRON MICROSCOPYf_angle_d0.75946980
ELECTRON MICROSCOPYf_dihedral_angle_d19.6244752
ELECTRON MICROSCOPYf_chiral_restr0.0525416
ELECTRON MICROSCOPYf_plane_restr0.0056064

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