[English] 日本語
Yorodumi
- EMDB-46627: Shigella flexneri bacteriophage B2 tail -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46627
TitleShigella flexneri bacteriophage B2 tail
Map data
Sample
  • Virus: Shigella phage B2 (virus)
    • Protein or peptide: Portal Protein Gp39
    • Protein or peptide: Head to tail adaptor Gp50
    • Protein or peptide: Gp34
    • Protein or peptide: Gp49
KeywordsB2 / VIRUS
Biological speciesShigella phage B2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSubramanian S / Bergland Drarvik SM / Parent KN
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140803 United States
National Science Foundation (NSF, United States)1750125 United States
CitationJournal: Sci Adv / Year: 2024
Title: Moo19 and B2: Structures of podophages with = 9 geometry and tailspikes with esterase activity.
Authors: Sundharraman Subramanian / Silje M Bergland Drarvik / Kendal R Tinney / Sarah M Doore / Kristin N Parent /
Abstract: Podophages are, by far, the least well studied of all the bacteriophages. Despite being classified together due to their short, noncontractile tails, there is a huge amount of diversity among members ...Podophages are, by far, the least well studied of all the bacteriophages. Despite being classified together due to their short, noncontractile tails, there is a huge amount of diversity among members of this group. Of the podophages, the N4-like family is the least well studied structurally and is quite divergent from well-characterized podophages such as T7 and P22. In this work, we isolate and fully characterize two members of the family by cryo-electron microscopy, genetics, and biochemistry. We describe the capsid features of Moo19 and B2, including a decoration protein. In addition, we have fully modeled the tail machinery for both phages and identify proteins with esterase activity. Genetic knockouts of the host reveal factors specific for host attachment including key modifications to the O-antigen on the lipopolysaccharide. Moo19 and B2 are both members, yet some distinct differences in the genome and structure place them into distinct clades.
History
DepositionAug 18, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46627.png

Downloads & links

-
Map

FileDownload / File: emd_46627.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 500 pix.
= 834. Å		1.67 Å/pix.
x 500 pix.
= 834. Å		1.67 Å/pix.
x 500 pix.
= 834. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.12042123 - 0.1829724
Average (Standard dev.)0.0001804685 (±0.0031425597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-249-249-249
Dimensions500500500
Spacing500500500
CellA=B=C: 834.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_46627_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_46627_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_46627_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Shigella phage B2

EntireName: Shigella phage B2 (virus)
Components
  • Virus: Shigella phage B2 (virus)
    • Protein or peptide: Portal Protein Gp39
    • Protein or peptide: Head to tail adaptor Gp50
    • Protein or peptide: Gp34
    • Protein or peptide: Gp49

-
Supramolecule #1: Shigella phage B2

SupramoleculeName: Shigella phage B2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2968270 / Sci species name: Shigella phage B2 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Shigella flexneri 2a str. 2457T (bacteria)

-
Macromolecule #1: Portal Protein Gp39

MacromoleculeName: Portal Protein Gp39 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage B2 (virus)
Molecular weightTheoretical: 79.127383 KDa
Recombinant expressionOrganism: Shigella flexneri 2a str. 2457T (bacteria)
SequenceString: MAKDELPIVN PEETGNLTDW DNEPTVSDLK SDYDSAYSSH SAQMSQITTW LNNLNVEGSA KPKKVPGRSS VQPMLIRKQA EWRYSALTE PFLSTDELFA VSPVTWEDRE AAIQNQLVLN YQFNIKIDKV RFIDDYVRNA VNEGTVIVRV GWCNYTQMVK E TVPVYAYY ...String:
MAKDELPIVN PEETGNLTDW DNEPTVSDLK SDYDSAYSSH SAQMSQITTW LNNLNVEGSA KPKKVPGRSS VQPMLIRKQA EWRYSALTE PFLSTDELFA VSPVTWEDRE AAIQNQLVLN YQFNIKIDKV RFIDDYVRNA VNEGTVIVRV GWCNYTQMVK E TVPVYAYY PAANEDQVAA LQEALQLKLE NPNAYNSLPD DIIASVDYSF ENRGAFVAVQ TGTEEVEYEK VIKNQPTVEV VN SQNVVID PTCNGDISQA QFVIYSFETS KSDLEKDGRY KNLDKISASM SNPLNTPDHQ VEDQSGFNFK DEPRKKFVAY EYW GWWDIN GNGKTVPIVA TFVGNTMIRL EENPFPDKKI PFVVVPYLPV PRSIYGEPDG ALLEDNQKII GATTRAMIDI LARS ANGQT GIRKDMLDVT NRRKFDKGED YEFNANVDPR QGIYMHVSPE IPQSAPMMIQ YQNNEAESLT GVKSFSQGIA SQALG DVAA GIRGALDAAS KRELGILRRL AQGVVEIGRK IISMNSEFLS EEEVVRVTNE QFVTVRRDEL AGEFDLKLSI STAEAD NQK AQELAFMLQT MGNSLPFEMS QMVLSDIARL RNMPDLAKRI ESYQPQPDPL AQRKAELEIA LLEAQIAETQ SKAIENR AS AGYKATQAQN VQSDTDLKNL DYVEQESGVK QARDVQKISA QAESQTQTKI VDYILKSGKP LSEI

-
Macromolecule #2: Head to tail adaptor Gp50

MacromoleculeName: Head to tail adaptor Gp50 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage B2 (virus)
Molecular weightTheoretical: 26.744287 KDa
Recombinant expressionOrganism: Shigella flexneri 2a str. 2457T (bacteria)
SequenceString: MKLSELFQML SVGELSLIRT GNDGQGIRTQ DYPKVIAQLN AGLTNLHARF PLLEKEVIIQ QYEQISKYYL RSEFAQMNTT STEKYKYLM DSPTERFLDD VIRVERVFDE CGCPLYLNNE PCCGSIVTPS FDCIQIVYPI ETNALFVTYR ANHPKIALTT T DLNTEVRI ...String:
MKLSELFQML SVGELSLIRT GNDGQGIRTQ DYPKVIAQLN AGLTNLHARF PLLEKEVIIQ QYEQISKYYL RSEFAQMNTT STEKYKYLM DSPTERFLDD VIRVERVFDE CGCPLYLNNE PCCGSIVTPS FDCIQIVYPI ETNALFVTYR ANHPKIALTT T DLNTEVRI PASHEKALTY YIASQLYSNS PNPETAAKGV EWSQRFEAEC TKIENLDLDN AHIAQTNVKP EMRGWV

-
Macromolecule #3: Gp34

MacromoleculeName: Gp34 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage B2 (virus)
Molecular weightTheoretical: 22.765822 KDa
Recombinant expressionOrganism: Shigella flexneri 2a str. 2457T (bacteria)
SequenceString: MAVVIEPITN EDLTTKVVDG TGIFDELMTA ANAHLSAQWD MERITGTQYA EVYLGQLTAV LQQAVTFLIE KDKTYLNNLL INAQIELAN KQIELADKEL EKADKEIELL ELNKELIAQK VKTEKAQISD TVDSVPVTGI IGAQIALYKQ QKDGFIRDAE Q KALKIISD ...String:
MAVVIEPITN EDLTTKVVDG TGIFDELMTA ANAHLSAQWD MERITGTQYA EVYLGQLTAV LQQAVTFLIE KDKTYLNNLL INAQIELAN KQIELADKEL EKADKEIELL ELNKELIAQK VKTEKAQISD TVDSVPVTGI IGAQIALYKQ QKDGFIRDAE Q KALKIISD TWITRKTVDD GTPLPTGFDT AAVDAFTRKV ADGVSVNY

-
Macromolecule #4: Gp49

MacromoleculeName: Gp49 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage B2 (virus)
Molecular weightTheoretical: 44.471602 KDa
Recombinant expressionOrganism: Shigella flexneri 2a str. 2457T (bacteria)
SequenceString: MIRTTNTCCG NQAGMVEKFI GTAYDVVKTV YDNLGEIQFI YNFLNDYGVL ITVDSVTELQ ELPTTAKYTR VYSSTPTGVR IYTDYLYVE GDRTGVLPSD PTATGSWVVV GSSNSGAATG TGAYIPFVFN NGSAAGGETT IVVPDYTIGV PEIYVEGFRQ Q VGRGFTFN ...String:
MIRTTNTCCG NQAGMVEKFI GTAYDVVKTV YDNLGEIQFI YNFLNDYGVL ITVDSVTELQ ELPTTAKYTR VYSSTPTGVR IYTDYLYVE GDRTGVLPSD PTATGSWVVV GSSNSGAATG TGAYIPFVFN NGSAAGGETT IVVPDYTIGV PEIYVEGFRQ Q VGRGFTFN SVNLTVTLAQ PLEQGDEVVL MLSGNPAVPD NPNIDSWTVI NWIYNNGAAV GGEQVIVIPY TFQTVPAIFK NG LRYQGGL STQSYTVDQD NKRILLTEPL STNDRLVVQL GGELVTLESP DRSLYEIARA TNMKDSEVIK SDNTVETLNG KRI LYDIVS QVYYWIPSSV PNNVYIQSVV NGQLTYLPGN IVVTLTPIVT LGLSGTTAQR PIGVLTGTQH FDTTLGKPIW FNGT AWVDS TGAVV

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
10.0 mMtris(hydroxymethyl)aminomethane
10.0 mMmagnesium chlorideMgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / 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: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133395
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