[English] 日本語
Yorodumi
- EMDB-32974: Capsid structure of Staphylococcus jumbo bacteriophage S6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32974
TitleCapsid structure of Staphylococcus jumbo bacteriophage S6
Map data
Sample
  • Virus: Staphylococcus phage S6 (virus)
    • Protein or peptide: Major structural protein ORF12
    • Protein or peptide: Hoc-like protein ORF90
KeywordsPhage / Phage head / CryoEM / Virus / Bacteriophage / Cryo-EM
Biological speciesStaphylococcus phage S6 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKoibuchi W / Uchiyama J / Matsuzaki S / Murata K / Iwasaki K / Miyazaki N
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: To Be Published
Title: Capsid structure of Staphylococcus jumbo bacteriophage S6
Authors: Koibuchi W / Uchiyama J / Matsuzaki S / Murata K / Iwasaki K / Miyazaki N
History
DepositionFeb 27, 2022-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32974.png

Downloads & links

-
Map

FileDownload / File: emd_32974.map.gz / Format: CCP4 / Size: 2.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 820 pix.
= 1394. Å		1.7 Å/pix.
x 820 pix.
= 1394. Å		1.7 Å/pix.
x 820 pix.
= 1394. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.09511126 - 0.20408665
Average (Standard dev.)0.0013133484 (±0.009095121)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-410-410-410
Dimensions820820820
Spacing820820820
CellA=B=C: 1394.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Staphylococcus phage S6

EntireName: Staphylococcus phage S6 (virus)
Components
  • Virus: Staphylococcus phage S6 (virus)
    • Protein or peptide: Major structural protein ORF12
    • Protein or peptide: Hoc-like protein ORF90

-
Supramolecule #1: Staphylococcus phage S6

SupramoleculeName: Staphylococcus phage S6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2913378 / Sci species name: Staphylococcus phage S6 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Name: Head / Diameter: 1300.0 Å / T number (triangulation number): 27

-
Macromolecule #1: Major structural protein ORF12

MacromoleculeName: Major structural protein ORF12 / type: protein_or_peptide / ID: 1 / Number of copies: 27 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage S6 (virus)
Molecular weightTheoretical: 59.259133 KDa
SequenceString: MLNPNRIKDE FSVRLEDIEN SINESYNLST IGGDFAAIAT DDAVFESYKD QLLEGFDAAE GEALAGMLDN TREEILMESS MGPIQPYAS LSMPILVKLW ARLALTEALP TQVANKPNFT VPILTPYVVD ADGNKHALPE SINNTPETLV GLVQIKEDIA V EGGKVTDY ...String:
MLNPNRIKDE FSVRLEDIEN SINESYNLST IGGDFAAIAT DDAVFESYKD QLLEGFDAAE GEALAGMLDN TREEILMESS MGPIQPYAS LSMPILVKLW ARLALTEALP TQVANKPNFT VPILTPYVVD ADGNKHALPE SINNTPETLV GLVQIKEDIA V EGGKVTDY DLFTGLKEGK EVRKGIDRLD RKFKIVEAKW SDSFDERTSA AGFVELGSNV VKLQDNDTLV GQIKYPTNGD GE VETDTIL GKVDVSSGEL TLTSASGKLT DVKVKGYVAS EQHTSATNVE LGLTRKDVVI DTAQHIEATV PLEVIQDMKA TYD IDGVAR LSETMSQLSS QKVDLDIIEF LDHEYKETDA KYHFSFDVFP HSDYSAHPKD WLEGLREVID HTTQSMKNDY KLYD VQFVI VGNPLDVRLI PNVSWTFNGG DRNADAYSNG IKINYSLGAA SGTANYRIIG SDLVRQGELT IIAIPQQDNY KTFMF YPYT FNVVNGGGYL NTRNPNVPNM MMTRRYTVES FVPIIGRITI KNNNGSVYAR

-
Macromolecule #2: Hoc-like protein ORF90

MacromoleculeName: Hoc-like protein ORF90 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage S6 (virus)
Molecular weightTheoretical: 53.151375 KDa
SequenceString: MATTNYFKVK LLDEKLIPFL GLGERGPREN VILSSNDLAS LKQAGWTVTD VQPLPETGKI KYDRRTVYFK SEGETGKFIN VPFYINPVD ARDVLGLLKF DLIKLSDKSV VKTYTAKDIK SEILSLPTSD LEVNEEYELK LYFPKDASEN YDIAISEGHK N LFERVKDS ...String:
MATTNYFKVK LLDEKLIPFL GLGERGPREN VILSSNDLAS LKQAGWTVTD VQPLPETGKI KYDRRTVYFK SEGETGKFIN VPFYINPVD ARDVLGLLKF DLIKLSDKSV VKTYTAKDIK SEILSLPTSD LEVNEEYELK LYFPKDASEN YDIAISEGHK N LFERVKDS VFIKVKEYGK FTGRLVQLQQ DINVLKESAL PLDKILGYKD FDTKEVTPVA KENLLQLLSV NVSDESYARY QA DKNRLLF FSKTGEILVK VIERSIQDNI VNFNIRILDE ETIQNEIDKK IEYSVYDPKD GKFESINQTK SITVTPETVN IEA EQTQKL EVTTEPEGRK VSFELKDGSE FASVDNNGNI TGISEGTANV TVKSDDVSKN VEVNVSRLKT KSLTVTPEEV NIDA ESTQQ LDVKIQPSTN SVSYSITEGS EYASVNNSGL VTAKAAGTAK VKVTSDSVSK DVSVTISTSQ VEETPEETTT E

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 27164
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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