[English] 日本語
Yorodumi
- EMDB-28176: Tail tip structure of Staphylococcus phage Andhra -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28176
TitleTail tip structure of Staphylococcus phage Andhra
Map data
Sample
  • Virus: Staphylococcus phage Andhra (virus)
    • Protein or peptide: gp1, tail tip protein
    • Protein or peptide: gp10, tail tip lysin (spike)EMD GP10
Function / homologyCHAP domain profile. / CHAP domain / CHAP domain / Peptidase
Function and homology information
Biological speciesStaphylococcus phage Andhra (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsKizziah JL / Hawkins NC / Dokland T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI156636 United States
CitationJournal: Sci Adv / Year: 2022
Title: Structure and host specificity of bacteriophage Andhra.
Authors: N'Toia C Hawkins / James L Kizziah / Asma Hatoum-Aslan / Terje Dokland /
Abstract: is an opportunistic pathogen of the human skin, often associated with infections of implanted medical devices. Staphylococcal picoviruses are a group of strictly lytic, short-tailed bacteriophages ... is an opportunistic pathogen of the human skin, often associated with infections of implanted medical devices. Staphylococcal picoviruses are a group of strictly lytic, short-tailed bacteriophages with compact genomes that are attractive candidates for therapeutic use. Here, we report the structure of the complete virion of -infecting phage Andhra, determined using high-resolution cryo-electron microscopy, allowing atomic modeling of 11 capsid and tail proteins. The capsid is a = 4 icosahedron containing a unique stabilizing capsid lining protein. The tail includes 12 trimers of a unique receptor binding protein (RBP), a lytic protein that also serves to anchor the RBPs to the tail stem, and a hexameric tail knob that acts as a gatekeeper for DNA ejection. Using structure prediction with AlphaFold, we identified the two proteins that comprise the tail tip heterooctamer. Our findings elucidate critical features for virion assembly, host recognition, and penetration.
History
DepositionSep 16, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28176.png

Downloads & links

-
Map

FileDownload / File: emd_28176.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.328 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.048139088 - 0.07593109
Average (Standard dev.)1.6834068e-05 (±0.0032397346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 339.968 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_28176_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_28176_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Staphylococcus phage Andhra

EntireName: Staphylococcus phage Andhra (virus)
Components
  • Virus: Staphylococcus phage Andhra (virus)
    • Protein or peptide: gp1, tail tip protein
    • Protein or peptide: gp10, tail tip lysin (spike)EMD GP10

-
Supramolecule #1: Staphylococcus phage Andhra

SupramoleculeName: Staphylococcus phage Andhra / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #2, #1 / NCBI-ID: 1958907 / Sci species name: Staphylococcus phage Andhra / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Staphylococcus epidermidis (bacteria)

-
Macromolecule #1: gp10, tail tip lysin (spike)

MacromoleculeName: gp10, tail tip lysin (spike) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 51.675402 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString: MNDKEKIDKF IHSNLNDDFG LSVDDLVGKV KGIGRFSAWC GNSSTKIKQV LNAVKSIGVS PALFAAYEKN EGYNGSWGWL NHTSPQGNY LTDAQFVARK LVSQSRQAGT PSWIDAGNPV DFVPASVKRK GNYDFSHNMK NGKVGRAYIP LTAAATWAAY Y PEGLQASY ...String:
MNDKEKIDKF IHSNLNDDFG LSVDDLVGKV KGIGRFSAWC GNSSTKIKQV LNAVKSIGVS PALFAAYEKN EGYNGSWGWL NHTSPQGNY LTDAQFVARK LVSQSRQAGT PSWIDAGNPV DFVPASVKRK GNYDFSHNMK NGKVGRAYIP LTAAATWAAY Y PEGLQASY NRVQNYGNPF LDAANTILGW GGKIDGKGGS SSGSSSSSSG TSGGLDVVAR AFEEFLKKLQ DSMQWDLHSI GT DKFFSNQ MFTITKTYNN TYRLNMNQKL LDEMKDLISR IDGGSGNDTG ADDSDGDHGG KAGKSVAPNG KSGRKIGGNW TYS NLPQKY KDAIEVPKFD PKYLAGSPFV NTGDTGQCTE LTWAYMHQIW GKRQPAWDNQ VTNGQRVWVV YRNQGARVTH RPTV GYGFS SKPNYLQAML PGVGHTGVVV AVFKDGSFLT ANYNVPPYWA PSRVVEYALI DGVPENAGDN IMFFSGIK

-
Macromolecule #2: gp1, tail tip protein

MacromoleculeName: gp1, tail tip protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 10.640743 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString:
VTNEKGQAYT EMLQLFNLLQ QWNDFYTAEN ANNLLVACQQ LLINYNEPVI KFINDENEDK SLLQYLAGDD GLAQWQFYKG FYNNYNVHI F

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98203
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more