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Yorodumi- EMDB-30778: Acidic stable capsid structure of Helicobacter pylori bacteriopha... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30778 | |||||||||
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Title | Acidic stable capsid structure of Helicobacter pylori bacteriophage KHP30 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CAPSID / PHAGE / PHAGE HEAD / CRYOEM / VIRUS | |||||||||
Function / homology | Protein of unknown function DUF4043 / Protein of unknown function (DUF4043) / Major structural protein ORF14 / Uncharacterized protein Function and homology information | |||||||||
Biological species | Helicobacter pylori bacteriophage KHP30 (virus) / Helicobacter phage KHP (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Kamiya R / Uchiyama J | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30778.map.gz | 308 MB | EMDB map data format | |
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Header (meta data) | emd-30778-v30.xml emd-30778.xml | 11 KB 11 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30778_fsc.xml | 26.2 KB | Display | FSC data file |
Images | emd_30778.png | 254.9 KB | ||
Filedesc metadata | emd-30778.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30778 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30778 | HTTPS FTP |
-Related structure data
Related structure data | 7dn2MC 7douC 7f2pC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_30778.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Helicobacter phage KHP
Entire | Name: Helicobacter phage KHP (virus) |
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Components |
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-Supramolecule #1: Helicobacter phage KHP
Supramolecule | Name: 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 |
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Virus shell | Shell ID: 1 / Name: Head / Diameter: 700.0 Å / T number (triangulation number): 9 |
-Macromolecule #1: Major structural protein ORF14
Macromolecule | Name: Major structural protein ORF14 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Helicobacter pylori bacteriophage KHP30 (virus) |
Molecular weight | Theoretical: 42.465922 KDa |
Sequence | String: MLEKLNNINF NNISNNLNLG IEVGREIQNA SWIKSPFFSI TGTGADRGVR LFSVASQQPF RPRIKAQLSG SGVSGNTDFE ANYDNLEIL SQTIYPDAFG NSLRSKIKAY SELERIDFIK ESVDSLTTWM NEERDKRIVA SLTNDFTNYL YTQTMNVATI R KAIFHARN ...String: MLEKLNNINF NNISNNLNLG IEVGREIQNA SWIKSPFFSI TGTGADRGVR LFSVASQQPF RPRIKAQLSG SGVSGNTDFE ANYDNLEIL SQTIYPDAFG NSLRSKIKAY SELERIDFIK ESVDSLTTWM NEERDKRIVA SLTNDFTNYL YTQTMNVATI R KAIFHARN GLKGDNSKAF PIKPIRATMQ SVGNVMVQNT SYIILLDSYQ ANQLKADSEF KELRKLYAFA GEDKGMLYSG LL GVIDNCP VIDAGVWNKF NVGMPNSSIS DSDFMRYLNK ANVSSIVTPR QFKEKLNQEK DEKKRSINKE ISIGCLIGAS AVL LAGSKE TRFYIDETVD AGRKSLVGVD CLLGVSKARY QSTDGVVTPY DNQDYAVIGL VSDME UniProtKB: Major structural protein ORF14 |
-Macromolecule #2: Cement protein gp15
Macromolecule | Name: Cement protein gp15 / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Helicobacter pylori bacteriophage KHP30 (virus) |
Molecular weight | Theoretical: 13.721461 KDa |
Sequence | String: MKQKVHSVSY LAKAEFKFNN GVYNLVALPS GAEVVKVSLE VVGNPIATST TSVSVGFEDE TTKNYFLTLD NLAVDDASKK HTTSAKDYT ATSNKVVVAE VKNANDNNVK GVLRVLYFLP SVIEVEY UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |