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- PDB-7dn2: Acidic stable capsid structure of Helicobacter pylori bacteriopha... -

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Basic information

Entry
Database: PDB / ID: 7dn2
TitleAcidic stable capsid structure of Helicobacter pylori bacteriophage KHP30
Components
  • Cement protein gp15
  • Major structural protein ORF14
KeywordsVIRUS / CAPSID / PHAGE / PHAGE HEAD / CRYOEM
Function / homologyProtein of unknown function DUF4043 / Phage capsid protein / Major structural protein ORF14 / Uncharacterized protein
Function and homology information
Biological speciesHelicobacter pylori bacteriophage KHP30 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 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
DepositionDec 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.0Oct 27, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 27, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Oct 27, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Oct 27, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 27, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 27, 2021Data content type: Primary map / Data content type: Primary map / Provider: 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 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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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
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Structure viewerMolecule:
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Assembly

Deposited unit
a: Major structural protein ORF14
b: Major structural protein ORF14
c: Major structural protein ORF14
d: Major structural protein ORF14
e: Major structural protein ORF14
f: Major structural protein ORF14
g: Major structural protein ORF14
h: Major structural protein ORF14
i: Major structural protein ORF14
1: Cement protein gp15
2: Cement protein gp15
3: Cement protein gp15
4: Cement protein gp15
5: Cement protein gp15
6: Cement protein gp15
7: Cement protein gp15
8: Cement protein gp15
9: Cement protein gp15


Theoretical massNumber of molelcules
Total (without water)505,68618
Polymers505,68618
Non-polymers00
Water00
1
a: Major structural protein ORF14
b: Major structural protein ORF14
c: Major structural protein ORF14
d: Major structural protein ORF14
e: Major structural protein ORF14
f: Major structural protein ORF14
g: Major structural protein ORF14
h: Major structural protein ORF14
i: Major structural protein ORF14
1: Cement protein gp15
2: Cement protein gp15
3: Cement protein gp15
4: Cement protein gp15
5: Cement protein gp15
6: Cement protein gp15
7: Cement protein gp15
8: Cement protein gp15
9: Cement protein gp15
x 60


Theoretical massNumber of molelcules
Total (without water)30,341,1871080
Polymers30,341,1871080
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
a: Major structural protein ORF14
b: Major structural protein ORF14
c: Major structural protein ORF14
d: Major structural protein ORF14
e: Major structural protein ORF14
f: Major structural protein ORF14
g: Major structural protein ORF14
h: Major structural protein ORF14
i: Major structural protein ORF14
1: Cement protein gp15
2: Cement protein gp15
3: Cement protein gp15
4: Cement protein gp15
5: Cement protein gp15
6: Cement protein gp15
7: Cement protein gp15
8: Cement protein gp15
9: Cement protein gp15
x 5


  • icosahedral pentamer
  • 2.53 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)2,528,43290
Polymers2,528,43290
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
a: Major structural protein ORF14
b: Major structural protein ORF14
c: Major structural protein ORF14
d: Major structural protein ORF14
e: Major structural protein ORF14
f: Major structural protein ORF14
g: Major structural protein ORF14
h: Major structural protein ORF14
i: Major structural protein ORF14
1: Cement protein gp15
2: Cement protein gp15
3: Cement protein gp15
4: Cement protein gp15
5: Cement protein gp15
6: Cement protein gp15
7: Cement protein gp15
8: Cement protein gp15
9: Cement protein gp15
x 6


  • icosahedral 23 hexamer
  • 3.03 MDa, 108 polymers
Theoretical massNumber of molelcules
Total (without water)3,034,119108
Polymers3,034,119108
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
Major structural protein ORF14


Mass: 42465.922 Da / Num. of mol.: 9 / Source method: isolated from a natural source
Source: (natural) Helicobacter pylori bacteriophage KHP30 (virus)
References: UniProt: I7H0H9
#2: Protein
Cement protein gp15


Mass: 13721.461 Da / Num. of mol.: 9 / Source method: isolated from a natural source
Source: (natural) Helicobacter pylori bacteriophage KHP30 (virus)
References: UniProt: I7HFW5
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 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
Image recordingAverage exposure time: 1 sec. / Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameCategory
8PHENIXmodel refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20737 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00735006
ELECTRON MICROSCOPYf_angle_d0.65247357
ELECTRON MICROSCOPYf_dihedral_angle_d9.53521167
ELECTRON MICROSCOPYf_chiral_restr0.0485457
ELECTRON MICROSCOPYf_plane_restr0.0046115

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