[English] 日本語
Yorodumi
- EMDB-15669: Jumbo Phage phi-kp24 tail outer sheath -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15669
TitleJumbo Phage phi-kp24 tail outer sheath
Map dataJumbo phage phi-kp24 tail outer sheath
Sample
  • Complex: Jumbo Phage phi-kp24 tail outer sheath
    • Protein or peptide: Putative tail sheath protein
KeywordsJumbo Phage / Klebsiella pneumoniae / tail / sheath / structural protein
Function / homology: / Bacteriophage phiKZ, gp29PR / Putative tail sheath protein / Putative virion structural protein
Function and homology information
Biological speciesKlebsiella phage vB_KpM_FBKp24 (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsOuyang R / Briegel A
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)84.034.014 Netherlands
CitationJournal: Nat Commun / Year: 2022
Title: High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers.
Authors: Ruochen Ouyang / Ana Rita Costa / C Keith Cassidy / Aleksandra Otwinowska / Vera C J Williams / Agnieszka Latka / Phill J Stansfeld / Zuzanna Drulis-Kawa / Yves Briers / Daniël M Pelt / ...Authors: Ruochen Ouyang / Ana Rita Costa / C Keith Cassidy / Aleksandra Otwinowska / Vera C J Williams / Agnieszka Latka / Phill J Stansfeld / Zuzanna Drulis-Kawa / Yves Briers / Daniël M Pelt / Stan J J Brouns / Ariane Briegel /
Abstract: The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combine cryo-electron microscopy methods, protein ...The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combine cryo-electron microscopy methods, protein structure prediction methods, molecular simulations, microbiological and machine learning approaches to explore the capsid, tail, and tail fibers of ϕKp24. We determine the structure of the capsid and tail at 4.1 Å and 3.0 Å resolution. We observe the tail fibers are branched and rearranged dramatically upon cell surface attachment. This complex configuration involves fourteen putative tail fibers with depolymerase activity that provide ϕKp24 with the ability to infect a broad panel of capsular polysaccharide (CPS) types of Klebsiella pneumoniae. Our study provides structural and functional insight into how ϕKp24 adapts to the variable surfaces of capsulated bacterial pathogens, which is useful for the development of phage therapy approaches against pan-drug resistant K. pneumoniae strains.
History
DepositionAug 25, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15669.png

Downloads & links

-
Map

FileDownload / File: emd_15669.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationJumbo phage phi-kp24 tail outer sheath
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 450 pix.
= 616.5 Å		1.37 Å/pix.
x 450 pix.
= 616.5 Å		1.37 Å/pix.
x 450 pix.
= 616.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0208
Minimum - Maximum-0.14429303 - 0.21090232
Average (Standard dev.)0.00048305813 (±0.0063263383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 616.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: 2

Fileemd_15669_half_map_1.map
Annotation2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: 1

Fileemd_15669_half_map_2.map
Annotation1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Jumbo Phage phi-kp24 tail outer sheath

EntireName: Jumbo Phage phi-kp24 tail outer sheath
Components
  • Complex: Jumbo Phage phi-kp24 tail outer sheath
    • Protein or peptide: Putative tail sheath protein

-
Supramolecule #1: Jumbo Phage phi-kp24 tail outer sheath

SupramoleculeName: Jumbo Phage phi-kp24 tail outer sheath / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The outer sheath in extension of Klebsiella Phage phi-kp24
Source (natural)Organism: Klebsiella phage vB_KpM_FBKp24 (virus)

-
Macromolecule #1: Putative tail sheath protein

MacromoleculeName: Putative tail sheath protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage vB_KpM_FBKp24 (virus)
Molecular weightTheoretical: 76.4025 KDa
SequenceString: MSEQITGSTP RIYYRGTKDS SVTRSTGSTT TLPLHRPLIM FFGQKGPTVP TWIDPVKFED IYGSETTNLS GVYCTHSTPF IKEAIAAGN QFMALRLEPS DIPDVATLGL SVDWVKTKID DYERNDDGTY KLDTNGDKIP LATQIDGIKF RFVLEKIETN E SGVSQYKK ...String:
MSEQITGSTP RIYYRGTKDS SVTRSTGSTT TLPLHRPLIM FFGQKGPTVP TWIDPVKFED IYGSETTNLS GVYCTHSTPF IKEAIAAGN QFMALRLEPS DIPDVATLGL SVDWVKTKID DYERNDDGTY KLDTNGDKIP LATQIDGIKF RFVLEKIETN E SGVSQYKK RTAKAGTIGT EATPSTITPL ADFRCRFKSS LGANTALRIW APTINSAQAA DADLQARIKS FLYRFQILTR AD KASSPTI FETIYNEPSL SVGFGENLVD PQTEVVYDFV ERIDSRYNDE DPSTYLMSPL DTPYLYQANI DSVLTAIQEL EAP FDTVSA DEDDLYQINL FGAQTVEGVP YHAVQILGVL DGGVTLTETA TNYLQGGGDG TLGNDSFNAA AYAVLSNLSN NAAF NITNY ARYPFNAFWD SGFDLKTKQT IPQLIGLRAD TWIALSTQDI SSDFNSNEEE ESIALSLMSR VSAFPDSSDF GTPAF RGMI VGGAGYYTET TRKLPVPLTL DRFRAYCRYA GASDGVLKPE YAVDEGDARK VQVVKSINNL DKSWRVRRAQ WNNNLV YVE DYDTNSQFYP GQQSFYSEQG SVLKAAIVGL CVANLNRFAF EAWRDLTGTQ KLTDDQLIER SDDAVSTRGT GAFDDRL IF TPHSEITQAD KERGYSWSMR IDFGANAFRT VMDMSSVAYT REELANG

UniProtKB: Putative tail sheath protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 39.03 Å
Applied symmetry - Helical parameters - Δ&Phi: 20.89 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 81869
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8au1:
Jumbo Phage phi-kp24 tail outer sheath

PDB-8bfk:
Jumbo Phage phi-kp24 tail inner tube

+
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