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- EMDB-30800: Acidic stable capsid structure of Helicobacter pylori bacteriopha... -

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Basic information

Entry
Database: EMDB / ID: EMD-30800
TitleAcidic stable capsid structure of Helicobacter pylori bacteriophage KHP40
Map data
Sample
  • Virus: Helicobacter phage KHP (virus)
    • Protein or peptide: Cement protein gp16
KeywordsCAPSID / PHAGE / PHAGE HEAD / CRYOEM / VIRUS
Function / homologyProtein of unknown function DUF4043 / Phage capsid protein / Uncharacterized protein / DUF4043 family protein
Function and homology information
Biological speciesHelicobacter phage KHP40 (virus) / Helicobacter phage KHP (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsKamiya R / Uchiyama J
Funding support Japan, 2 items
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 17, 2020-
Header (metadata) releaseOct 27, 2021-
Map releaseOct 27, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dou
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7f2p
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7dou
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7f2p
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30800.png

Downloads & links

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Map

FileDownload / File: emd_30800.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 750 pix.
= 870. Å		1.16 Å/pix.
x 750 pix.
= 870. Å		1.16 Å/pix.
x 750 pix.
= 870. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.08803996 - 0.16528526
Average (Standard dev.)0.0006209508 (±0.007930677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-375-375-375
Dimensions750750750
Spacing750750750
CellA=B=C: 870.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z750750750
origin x/y/z0.0000.0000.000
length x/y/z870.000870.000870.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-375-375-375
NC/NR/NS750750750
D min/max/mean-0.0880.1650.001

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Supplemental data

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Sample components

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Entire : Helicobacter phage KHP

EntireName: Helicobacter phage KHP (virus)
Components
  • Virus: Helicobacter phage KHP (virus)
    • Protein or peptide: Cement protein gp16

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Supramolecule #1: Helicobacter phage KHP

SupramoleculeName: Helicobacter phage KHP / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1208236 / Sci species name: Helicobacter phage KHP / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Name: Head / Diameter: 700.0 Å / T number (triangulation number): 9

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Macromolecule #1: Cement protein gp16

MacromoleculeName: Cement protein gp16 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter phage KHP40 (virus)
Molecular weightTheoretical: 13.469469 KDa
SequenceString:
MKQKVHSVSY LAKAEFEYKN GVYDLVALPT GAEVIKISLE VVGLPTAGHV SVGFKDESKK NYSSILTLPV NETSGVVTKD YTVKSDKIV AAEVKDALAE GSDGRPVKCV LRALYFLPSV IEVEY

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 6772
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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