[English] 日本語
Yorodumi
- EMDB-22088: Structure of the Campylobacter jejuni G508A Flagellar Filament -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22088
TitleStructure of the Campylobacter jejuni G508A Flagellar Filament
Map data
Sample
  • Organelle or cellular component: Bacterial Flagellar Filament
    • Protein or peptide: Flagellin A
  • Ligand: 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid
KeywordsHelical Symmetry / Bacterial Flagellar Filament / STRUCTURAL PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin hook, IN motif / Flagellin hook IN motif / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Biological speciesCampylobacter jejuni (Campylobacter)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKreutzberger MAB / Wang F / Egelman EH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM080186 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Atomic structure of the Campylobacter jejuni flagellar filament reveals how epsilon Proteobacteria escaped Toll-like receptor 5 surveillance.
Authors: Kreutzberger MAB / Ewing C / Poly F / Wang F / Egelman EH
History
DepositionJun 1, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0054
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0054
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6x80
  • Surface level: 0.0054
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6x80
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

-
Map

FileDownload / File: emd_22088.map.gz / Format: CCP4 / Size: 236.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.0054 / Movie #1: 0.0054
Minimum - Maximum-0.0080477325 - 0.019455412
Average (Standard dev.)0.00032223167 (±0.0016402273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384420
Spacing384384420
CellA: 414.72003 Å / B: 414.72003 Å / C: 453.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z384384420
origin x/y/z0.0000.0000.000
length x/y/z414.720414.720453.600
α/β/γ90.00090.00090.000
start NX/NY/NZ777686
NX/NY/NZ10710993
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384420
D min/max/mean-0.0080.0190.000

-
Supplemental data

-
Sample components

-
Entire : Bacterial Flagellar Filament

EntireName: Bacterial Flagellar Filament
Components
  • Organelle or cellular component: Bacterial Flagellar Filament
    • Protein or peptide: Flagellin A
  • Ligand: 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid

-
Supramolecule #1: Bacterial Flagellar Filament

SupramoleculeName: Bacterial Flagellar Filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Campylobacter jejuni (Campylobacter)

-
Macromolecule #1: Flagellin A

MacromoleculeName: Flagellin A / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
Molecular weightTheoretical: 59.590762 KDa
Recombinant expressionOrganism: Campylobacter jejuni (Campylobacter)
SequenceString: MGFRINTNVA ALNAKANSDL NAKSLDASLS RLSSGLRINS AADDASGMAI ADSLRSQANT LGQAISNGND ALGILQTADK AMDEQLKIL DTIKTKATQA AQDGQSLKTR TMLQADINKL MEELDNIANT TSFNGKQLLS GNFTNQEFQI GASSNQTVKA T IGATQSSK ...String:
MGFRINTNVA ALNAKANSDL NAKSLDASLS RLSSGLRINS AADDASGMAI ADSLRSQANT LGQAISNGND ALGILQTADK AMDEQLKIL DTIKTKATQA AQDGQSLKTR TMLQADINKL MEELDNIANT TSFNGKQLLS GNFTNQEFQI GASSNQTVKA T IGATQSSK IGVTRFETGA QSFTSGVVGL TIKNYNGIED FKFDNVVIST SVGTGLGALA EEINKSADKT GVRATYDVKT TG VYAIKEG TTSQDFAING VTIGKIEYKD GDGNGSLISA INAVKDTTGV QASKDENGKL VLTSADGRGI KITGDIGVGS GIL ANQKEN YGRLSLVKND GRDINISGTN LSAIGMGTTD MISQSSVSLR ESKGQISATN ADAMGFNSYK GGGKFVFTQN VSSI SAFMS AQGSGFSRGS GFSVGSGKNL SVGLSQGIQI ISSAASMSNT YVVSAGSGFS SGSGNSQFAA LKTTAANTTD ETAGV TTLK GAMAVMDIAE TAITNLDQIR ADIASIQNQV TSTINNITVT QVNVKAAESQ IRDVDFASES ANYSKANILA QSGSYA MAQ ANSSQQNVLR LLQ

UniProtKB: Flagellin A

-
Macromolecule #2: 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulop...

MacromoleculeName: 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid
type: ligand / ID: 2 / Number of copies: 374 / Formula: P8E
Molecular weightTheoretical: 250.249 Da
Chemical component information

ChemComp-P8E:
5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.0 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

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.32 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software: (Name: SPIDER, RELION) / Details: MODEL:MAP FSC using a threshold of 0.5 / Number images used: 116959
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: averaged cylinder using all segments, with random azimuthal angles
Final angle assignmentType: NOT APPLICABLE

+
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