[English] 日本語
Yorodumi
- EMDB-10362: Cryo-EM structure of the wild-type flagellar filament of the Firm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10362
TitleCryo-EM structure of the wild-type flagellar filament of the Firmicute Kurthia
Map data
Sample
  • Complex: Flagellar Filament
    • Protein or peptide: Flagellin
KeywordsGram-Positive Bacteria Flagella / Helical / Wild-Type / protein fibril
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
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 speciesKurthia sp. 11kri321 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBlum TB / Abrahams JP
Funding support Switzerland, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_17002 Switzerland
Swiss National Science Foundation200021_165669 Switzerland
Swiss National Science Foundation31003A_152972 Switzerland
Swiss National Science Foundation31003A_179297 Switzerland
CitationJournal: Sci Rep / Year: 2019
Title: The wild-type flagellar filament of the Firmicute Kurthia at 2.8 Å resolution in vivo.
Authors: Thorsten B Blum / Sevasti Filippidou / Mathilda Fatton / Pilar Junier / Jan Pieter Abrahams /
Abstract: Bacteria swim and swarm by rotating the micrometers long, helical filaments of their flagella. They change direction by reversing their flagellar rotation, which switches the handedness of the ...Bacteria swim and swarm by rotating the micrometers long, helical filaments of their flagella. They change direction by reversing their flagellar rotation, which switches the handedness of the filament's supercoil. So far, all studied functional filaments are composed of a mixture of L- and R-state flagellin monomers. Here we show in a study of the wild type Firmicute Kurthia sp., that curved, functional filaments can adopt a conformation in vivo that is closely related to a uniform, all-L-state. This sheds additional light on transitions of the flagellar supercoil and uniquely reveals the atomic structure of a wild-type flagellar filament in vivo, including six residues showing clearly densities of O-linked glycosylation.
History
DepositionOct 3, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseOct 30, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0244
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0244
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6t17
  • Surface level: 0.0244
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6t17
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10362.png

Downloads & links

-
Map

FileDownload / File: emd_10362.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 270.848 Å		1.06 Å/pix.
x 256 pix.
= 270.848 Å		1.06 Å/pix.
x 256 pix.
= 270.848 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0244 / Movie #1: 0.0244
Minimum - Maximum-0.023902241 - 0.061274417
Average (Standard dev.)0.00032706262 (±0.005256356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.848 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0581.0581.058
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z270.848270.848270.848
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ307236
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0240.0610.000

-
Supplemental data

-
Sample components

-
Entire : Flagellar Filament

EntireName: Flagellar Filament
Components
  • Complex: Flagellar Filament
    • Protein or peptide: Flagellin

-
Supramolecule #1: Flagellar Filament

SupramoleculeName: Flagellar Filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Kurthia sp. 11kri321 (bacteria)

-
Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 44 / Enantiomer: LEVO
Source (natural)Organism: Kurthia sp. 11kri321 (bacteria)
Molecular weightTheoretical: 29.530055 KDa
Recombinant expressionOrganism: Kurthia sp. 11kri321 (bacteria)
SequenceString: MRIQHNIAAL NTHRNLAANN AAASKNLEKL SSGFKINRAG DDAAGLAISE KMRGQISGLN MASKNSSDAI SLIQTAEGGL NETHAILQR MRELAVQSRN DTNDEATNDR SNLNDELKQL QEEITRISSQ MEFNNKKLLD GSQSTNGLTF QIGANAGQTI T MKISTMSA ...String:
MRIQHNIAAL NTHRNLAANN AAASKNLEKL SSGFKINRAG DDAAGLAISE KMRGQISGLN MASKNSSDAI SLIQTAEGGL NETHAILQR MRELAVQSRN DTNDEATNDR SNLNDELKQL QEEITRISSQ MEFNNKKLLD GSQSTNGLTF QIGANAGQTI T MKISTMSA TKLGVDAAKA SISKGTAASK AIKSIDDAIN TVSKTRSALG AVQNRLEHTI NNLGTSAENL TAAESRIRDT DM AAEMMAF TKNNILTQAA QSMLAQANQQ PQGVLQLLQ

UniProtKB: Flagellin

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 86.0 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 reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.83 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.45 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9270
Startup modelType of model: OTHER / Details: Sub-tomogram average
Final angle assignmentType: NOT APPLICABLE
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