[English] 日本語
Yorodumi
- EMDB-12874: CryoEM structure of the outer membrane secretin pore pIV from the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12874
TitleCryoEM structure of the outer membrane secretin pore pIV from the f1 filamentous bacteriophage.
Map dataPostprocessed masked map from Relion
Sample
  • Organelle or cellular component: Virion export protein pIV
    • Protein or peptide: Virion export protein
  • Ligand: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
KeywordsSecretin Outer membrane Virion export / VIRAL PROTEIN
Function / homology
Function and homology information


viral extrusion / protein secretion / host cell membrane / membrane
Similarity search - Function
: / GspD-like, N0 domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein
Similarity search - Domain/homology
Virion export protein
Similarity search - Component
Biological speciesInoviridae sp. (virus) / Enterobacteria phage f1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsConners R / Gold VAM
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust210363/Z/18/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: CryoEM structure of the outer membrane secretin channel pIV from the f1 filamentous bacteriophage.
Authors: Rebecca Conners / Mathew McLaren / Urszula Łapińska / Kelly Sanders / M Rhia L Stone / Mark A T Blaskovich / Stefano Pagliara / Bertram Daum / Jasna Rakonjac / Vicki A M Gold /
Abstract: The Ff family of filamentous bacteriophages infect gram-negative bacteria, but do not cause lysis of their host cell. Instead, new virions are extruded via the phage-encoded pIV protein, which has ...The Ff family of filamentous bacteriophages infect gram-negative bacteria, but do not cause lysis of their host cell. Instead, new virions are extruded via the phage-encoded pIV protein, which has homology with bacterial secretins. Here, we determine the structure of pIV from the f1 filamentous bacteriophage at 2.7 Å resolution by cryo-electron microscopy, the first near-atomic structure of a phage secretin. Fifteen f1 pIV subunits assemble to form a gated channel in the bacterial outer membrane, with associated soluble domains projecting into the periplasm. We model channel opening and propose a mechanism for phage egress. By single-cell microfluidics experiments, we demonstrate the potential for secretins such as pIV to be used as adjuvants to increase the uptake and efficacy of antibiotics in bacteria. Finally, we compare the f1 pIV structure to its homologues to reveal similarities and differences between phage and bacterial secretins.
History
DepositionMay 5, 2021-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0226
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0226
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ofh
  • Surface level: 0.0226
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ofh
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12874.png

Downloads & links

-
Map

FileDownload / File: emd_12874.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed masked map from Relion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 224 pix.
= 240.128 Å		1.07 Å/pix.
x 224 pix.
= 240.128 Å		1.07 Å/pix.
x 224 pix.
= 240.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0226 / Movie #1: 0.0226
Minimum - Maximum-0.10828287 - 0.17869703
Average (Standard dev.)0.00061690575 (±0.007471375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 240.128 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0721.0721.072
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z240.128240.128240.128
α/β/γ90.00090.00090.000
start NX/NY/NZ799196
NX/NY/NZ149138117
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.1080.1790.001

-
Supplemental data

-
Additional map: Postprocessed map after DeepEMhancer

Fileemd_12874_additional_1.map
AnnotationPostprocessed map after DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half map1

Fileemd_12874_additional_2.map
AnnotationHalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half map2

Fileemd_12874_additional_3.map
AnnotationHalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Virion export protein pIV

EntireName: Virion export protein pIV
Components
  • Organelle or cellular component: Virion export protein pIV
    • Protein or peptide: Virion export protein
  • Ligand: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE

-
Supramolecule #1: Virion export protein pIV

SupramoleculeName: Virion export protein pIV / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: From Inoviridae sp. f1
Source (natural)Organism: Inoviridae sp. (virus)
Molecular weightTheoretical: 669.7 KDa

-
Macromolecule #1: Virion export protein

MacromoleculeName: Virion export protein / type: protein_or_peptide / ID: 1
Details: S9P, D49N, I66N are naturally occurring polymorphisms.
Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage f1 (virus)
Molecular weightTheoretical: 44.657707 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QVIEMNNSPL RDFVTWYSKQ TGESVIVSPD VKGTVTVYSS DVKPENLRNF FISVLRANNF DMVGSNPSII QKYNPNNQDY IDELPSSDN QEYDDNSAPS GGFFVPQNDN VTQTFKINNV RAKDLIRVVE LFVKSNTSKS SNVLSVDGSN LLVVSAPKDI L DNLPQFLS ...String:
QVIEMNNSPL RDFVTWYSKQ TGESVIVSPD VKGTVTVYSS DVKPENLRNF FISVLRANNF DMVGSNPSII QKYNPNNQDY IDELPSSDN QEYDDNSAPS GGFFVPQNDN VTQTFKINNV RAKDLIRVVE LFVKSNTSKS SNVLSVDGSN LLVVSAPKDI L DNLPQFLS TVDLPTDQIL IEGLIFEVQQ GDALDFSFAA GSQRGTVAGG VNTDRLTSVL SSAGGSFGIF NGDVLGLSVR AL KTNSHSK ILSVPRILTL SGQKGSISVG QNVPFITGRV TGESANVNNP FQTVERQNVG ISMSVFPVAM ASAHHHHHHH GGN IVLDIT IKADSLSSST QASDVITNQR SIATTVNLRD GQTLLLGGLT DYKNTSQDSG VPFLSKIPLI GLLFSSRSDS NEES TLYVL VKATIVRAL

UniProtKB: Virion export protein

-
Macromolecule #2: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE

MacromoleculeName: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
type: ligand / ID: 2 / Number of copies: 30 / Formula: CPS
Molecular weightTheoretical: 614.877 Da
Chemical component information

ChemComp-CPS:
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / detergent*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.7 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
1.0 % (w/v)C32H58N2O7SCHAPS (3-((3-cholamidopropyl) dimethylammonio)-1-propanesulfonate)
25.0 mMC8H17N2NaO4Ssodium hepes
500.0 mMNaClsodium chloride
0.5 mMC10H16N2O8EDTA
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: LACEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 0, blot time 4sec.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 3.52 sec. / Average electron dose: 42.059 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1beta) / Number images used: 111679
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1beta)
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5w68


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7ofh:
CryoEM structure of the outer membrane secretin pore pIV from the f1 filamentous bacteriophage.

+
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