[English] 日本語
Yorodumi
- EMDB-11734: Cryo-EM structure of an extracellular contractile injection syste... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11734
TitleCryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the cap portion in extended state.
Map data
Sample
  • Complex: The cap portion of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis
    • Protein or peptide: cap protein (Algo1)
    • Protein or peptide: cap adaptor protein (Algo2)
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Putative phage tail sheath protein FI
Keywordsextracellular contractile injection system / STRUCTURAL PROTEIN
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Pvc16, N-terminal / Pvc16 N-terminal domain / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Phage tail protein / Putative phage tail sheath protein FI / Uncharacterized protein / Pvc16 N-terminal domain-containing protein
Similarity search - Component
Biological speciesAlgoriphagus machipongonensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsXu J / Ericson C
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
European Research Council (ERC) Switzerland
Swiss National Science Foundation Switzerland
Other private Switzerland
CitationJournal: Nat Microbiol / Year: 2022
Title: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis.
Authors: Jingwei Xu / Charles F Ericson / Yun-Wei Lien / Florentine U N Rutaganira / Fabian Eisenstein / Miki Feldmüller / Nicole King / Martin Pilhofer /
Abstract: Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). ...Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a 'cap adaptor' located at the distal end, a 'plug' exposed to the tube lumen, and a 'cage' formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re-engineering CISs.
History
DepositionSep 17, 2020-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7adz
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7adz
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11734.png

Downloads & links

-
Map

FileDownload / File: emd_11734.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.11590661 - 0.21310976
Average (Standard dev.)0.00043434527 (±0.0070644855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z440.000440.000440.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1160.2130.000

-
Supplemental data

-
Sample components

-
Entire : The cap portion of an extracellular contractile injection system ...

EntireName: The cap portion of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis
Components
  • Complex: The cap portion of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis
    • Protein or peptide: cap protein (Algo1)
    • Protein or peptide: cap adaptor protein (Algo2)
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Putative phage tail sheath protein FI

-
Supramolecule #1: The cap portion of an extracellular contractile injection system ...

SupramoleculeName: The cap portion of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)

-
Macromolecule #1: cap protein (Algo1)

MacromoleculeName: cap protein (Algo1) / type: protein_or_peptide / ID: 1 / Details: cap protein (Algo1) / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 22.981086 KDa
SequenceString: MIFEVLKILT DEVNQNFKGL EMEDSEVVLN NVALIDSQQD VATELQNKVI LSMINLREEV TMKNFPNNVL EGTKVTYKNP KLNINLFLI FCANRTGYKK SLSDLSRILE FFQHKSVFTQ SNTSFDRDLE EMENVKNFRF TMELFTPTFE ELNYIWGTLG G RQYPSVFY ...String:
MIFEVLKILT DEVNQNFKGL EMEDSEVVLN NVALIDSQQD VATELQNKVI LSMINLREEV TMKNFPNNVL EGTKVTYKNP KLNINLFLI FCANRTGYKK SLSDLSRILE FFQHKSVFTQ SNTSFDRDLE EMENVKNFRF TMELFTPTFE ELNYIWGTLG G RQYPSVFY KLNLIVIDRD ATTSEEGVIT NIHRNYETL

UniProtKB: Pvc16 N-terminal domain-containing protein

-
Macromolecule #2: cap adaptor protein (Algo2)

MacromoleculeName: cap adaptor protein (Algo2) / type: protein_or_peptide / ID: 2 / Details: cap adaptor protein (Algo2) / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 33.083371 KDa
SequenceString: MQVSSSFRSF LKLDILHSYF LNDGEKDFSS MNEEESKTQL KSYNWKDFLE IYPSQKTSHM MRGNKIFFKS FNDSIILAIK VESGTENQP FNELYEDESM TFLLSLKDQY FGNYTDLDLA DQLLYFSNKT PVLPEAFTFK PIDRINQSGT VGEEYLYEGE N KKHLLEEA ...String:
MQVSSSFRSF LKLDILHSYF LNDGEKDFSS MNEEESKTQL KSYNWKDFLE IYPSQKTSHM MRGNKIFFKS FNDSIILAIK VESGTENQP FNELYEDESM TFLLSLKDQY FGNYTDLDLA DQLLYFSNKT PVLPEAFTFK PIDRINQSGT VGEEYLYEGE N KKHLLEEA HLNPGGGVLG IIQIYMKGDT PVLSLINNDG TLKNSLPHFK IHFSNRKSTW KYINLKDDFE TETKKDYPLT KF GFILLDK KSDFISPPAH FEKYVFPNPD ARRIKITPTK NYSEIFI

UniProtKB: Uncharacterized protein

-
Macromolecule #3: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 16.375458 KDa
SequenceString:
MSYPLSKFHF SVEWGGTKIG FTEVSGLDLE TEIIEYRHGA SPEYSKIKMP GMQKFSNITL KRGTFKSDNE YFQWYNTINL NKVERRDLT ISLLNEEHEP VVTWKVKNAW PLKVQSTDLK GDGNEVAIES MELAHEGLVI QNE

UniProtKB: Phage tail protein

-
Macromolecule #4: Putative phage tail sheath protein FI

MacromoleculeName: Putative phage tail sheath protein FI / type: protein_or_peptide / ID: 4
Details: the residues (288-320aa) are not built up in the model and the residues (430-446aa) are assigned as poly-alanine due to the poor density map.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 76.319039 KDa
SequenceString: MATYKTPGVY IEEITKFPPS VAQVETAIPA FIGYTQFART KPSVDSDDLI LKPKRISSLL DFTTYYGGAQ NEQGITVKLT DTLIEGAEN RTINVPEPTF KSPYLMFYSL QMYFANGGGP CYIVSTGVYD DWSDSETPPT INFSDLESGL AVIRKEDEPT L LLFPDATN ...String:
MATYKTPGVY IEEITKFPPS VAQVETAIPA FIGYTQFART KPSVDSDDLI LKPKRISSLL DFTTYYGGAQ NEQGITVKLT DTLIEGAEN RTINVPEPTF KSPYLMFYSL QMYFANGGGP CYIVSTGVYD DWSDSETPPT INFSDLESGL AVIRKEDEPT L LLFPDATN LPTDDEFYSL YNSALMQCND LQDRFTILDT YSDQTYNDGV EDLDPIPALR NGINLTKDYL KYGAAYYPFV QT ILNYQYS ADEIVIQHLS YNPNAIATAL DNLNAVNGPT FIDAILDDLR DLSLPDISGE ISDAVGFMYD DVDGFDIDGT FTT NSVKVA NFASLVESVL STLNELIDAK EEINKDVNSA IASSEEDNAI KTAISDALDV FNEDFEGADK IESVAKNLSD LLIK IKQAD TNTKVENVLS INALNFSAEF EKLLTYDVNT GLTASVTLDL FANIGTRLDD IIAAVSAAEP IDVNNGKLNG RLLSD IEPL DNATYNTILL EINSHKVTLP PSSSMAGAYA RVDNDRGVWK SPANIGLNYV SKPSVTVSHE EQESMNVHGT GKSVNA IRS FVGKGTLVWG ARTLAGNDNE WRYISVRRFF NMAEESIKKA TEQFVFEPND GNTWVRVRAM IENFLILQWR AGALAGA KP EHAFYVKVGL GQTMTAQDIL EGNMNVEIGL AVVRPAEFII LKFSHKMQES

UniProtKB: Putative phage tail sheath protein FI

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

9763

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65059
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7adz:
Cryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the cap portion in extended state.

+
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