[English] 日本語
Yorodumi
- EMDB-19974: Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19974
TitleCryo-EM structure of Staphylococcus aureus bacteriophage phi812 central spike protein - knob and petal domains
Map dataPhage phi812 central spike protein - knob and petal domains; postprocessed map
Sample
  • Complex: Central spike protein - knob and petal domains
    • Protein or peptide: GP-PDE domain-containing protein
Keywordsbacteriophage / phage / contractile / phi812 / spike / central spike / TIM / VIRAL PROTEIN
Function / homologyGlycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / GP-PDE domain-containing protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsBinovsky J / Pichel-Beleiro A / van Raaij MJ / Plevka P
Funding supportEuropean Union, Czech Republic, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103 Czech Republic
CitationJournal: EMBO J / Year: 2026
Title: Conformational changes of the baseplate regulating tail contraction of Staphylococcus phage 812.
Authors: Ján Bíňovský / Marta Šiborová / Maryna Zlatohurska / Jiří Nováček / Pavol Bárdy / Roman Baška / Karel Škubník / Tibor Botka / Martin Benešík / Roman Pantůček / Konstantinos ...Authors: Ján Bíňovský / Marta Šiborová / Maryna Zlatohurska / Jiří Nováček / Pavol Bárdy / Roman Baška / Karel Škubník / Tibor Botka / Martin Benešík / Roman Pantůček / Konstantinos Tripsianes / Pavel Plevka /
Abstract: Phages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of ...Phages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of phage 812, a member of the Kayvirus genus, which infects Gram-positive Staphylococcus strains, is formed of a core, wedge modules, and baseplate arms carrying receptor-binding proteins 1 and 2 and tripod complexes. Upon binding to a host cell, the receptor-binding proteins of phage 812 baseplate reorient and undergo conformational changes. The changes to the tripod complexes trigger the release of the central spike and weld proteins, which expose peptidoglycan-degrading domains of the hub proteins. Changes in the positions of baseplate arms are transmitted through wedge modules to tail sheath initiator proteins. The ring of the tail sheath initiator proteins expands and triggers the contraction of the tail sheath, which shortens to 50% and pushes the tail tube 10-30 nm into the bacterial cytoplasm. Homologous molecular mechanisms are probably shared by phages of the Herelleviridae family with contractile tails to infect Gram-positive bacteria.
History
DepositionMar 27, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19974.png

Downloads & links

-
Map

FileDownload / File: emd_19974.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage phi812 central spike protein - knob and petal domains; postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.027909704 - 0.06598589
Average (Standard dev.)0.000112777365 (±0.0013928787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_19974_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Phage phi812 central spike protein - knob and...

Fileemd_19974_half_map_1.map
AnnotationPhage phi812 central spike protein - knob and petal domains; half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Phage phi812 central spike protein - knob and...

Fileemd_19974_half_map_2.map
AnnotationPhage phi812 central spike protein - knob and petal domains; half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Central spike protein - knob and petal domains

EntireName: Central spike protein - knob and petal domains
Components
  • Complex: Central spike protein - knob and petal domains
    • Protein or peptide: GP-PDE domain-containing protein

-
Supramolecule #1: Central spike protein - knob and petal domains

SupramoleculeName: Central spike protein - knob and petal domains / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus phage 812 (virus)

-
Macromolecule #1: GP-PDE domain-containing protein

MacromoleculeName: GP-PDE domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 94.274195 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSDDLNVKGL VLATVSKINY KYQSVEVKVN NLTLGSRIGD DGSLAVPYPK SFIGRTPEGS VFGTKPLITE GSVVLIGFLN DDINSPIIL SVYGDNEQNK MINTNPLDGG KFDTESVYKY SSSLYEILPS LNYKYDDGEG TSIRTYNGKS FFSMTSGEEE K PQATDFYT ...String:
GSDDLNVKGL VLATVSKINY KYQSVEVKVN NLTLGSRIGD DGSLAVPYPK SFIGRTPEGS VFGTKPLITE GSVVLIGFLN DDINSPIIL SVYGDNEQNK MINTNPLDGG KFDTESVYKY SSSLYEILPS LNYKYDDGEG TSIRTYNGKS FFSMTSGEEE K PQATDFYT GTEYQDLFTS YYGNKTLIEP RIQKAPNMLF KHQGVFYDDG TPDNHITTLF ISERGDIRAS VLNTETQKRT TQ EMSSDGS YRVIKQDDDL MLDEAQVWIE YGISEDNKFY IKNDKHKFEF TDEGIYIDDK PMLENLDESI AEAMKNLNEI QKE LDDINY LLKGVGKDNL EELIESTKES IEASKKATSD VNRLTTQIAE VSGRTEGIIT QFQKFRDETF KDFYEDASTV INEV NQNFP TMKTDVKTLK TKVDNLEKTE IPNIKTRLTE LENNNNNADK IISDRGEHIG AMIQLEENVT VPMRKYMPIP WSKVT YNNA EFWDSNNPTR LVVPKGITKV RVAGNVLWDS NATGQRMLRI LKNGTYSIGL PYTRDVAIST APQNGTSGVI PVKEGD YFE FEAFQDSEGD RQFRADPYTW FSIEAIELET ETMEKDFMLI GHRGATGYTD EHTIKGYQMA LDKGADYIEL DLQLTKD NK LLCMHDSTID RTTTGTGKVG DMTLSYIQTN FTSLNGEPIP SLDDVLNHFG TKVKYYIETK RPFDANMDRE LLTQLKAK G LIGIGSERFQ VIIQSFARES LINIHNQFSN IPLAYLTSTF SESEMDDCLS YGFYAIAPKY TTITKELVDL AHSKGLKVH AWTVNTKEEM QSLIQMGVDG FFTNYLDEYK KI

UniProtKB: GP-PDE domain-containing protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
50.0 mMKNaO4P-Sodium Potassium Phosphate
200.0 mMNaClSodium Chloride

Details: sample diluted 10x with water before vitrification
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Detailssample diluted 10x with water before vitrification

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 3120 / Average exposure time: 8.0 sec. / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 487160
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Initial model generated by stochastic gradient descent in Relion
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0beta) / Number images used: 135736
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Details: 3D Autorefine
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0beta) / Details: 3D Autorefine
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
ChainDetails
source_name: Other, initial_model_type: experimental modelXray structure
source_name: Other, initial_model_type: in silico modelmanual building
DetailsChimera; Isolde
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9eul:
Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 central spike protein - knob and petal domains

+
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