[English] 日本語
Yorodumi
- EMDB-45505: Caulobacter crescentus FljJM flagellar filament (asymmetrical) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45505
TitleCaulobacter crescentus FljJM flagellar filament (asymmetrical)
Map data
Sample
  • Complex: FljJM flagellar filament (asymmetrical)
    • Protein or peptide: Flagellin FljM
Keywordsflagellin / flagellar filament / STRUCTURAL PROTEIN
Function / homologyFlagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / bacterial-type flagellum / structural molecule activity / extracellular region / Flagellin FljM
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsSanchez JC / Montemayor EJ / Ploscariu NT / Parrell D / Baumgardt JK / Yang JE / Sibert B / Cai K / Wright ER
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM104540 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM139168 United States
Department of Energy (DOE, United States)DE-SC0018409 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM135066 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM143854 United States
CitationJournal: To Be Published
Title: Direct evidence for multi-flagellin filament stabilization via atomic-level architecture of Caulobacter crescentus flagellar filaments
Authors: Sanchez JC / Montemayor EJ / Ploscariu NT / Parrell D / Baumgardt JK / Yang JE / Sibert B / Cai K / Wright ER
History
DepositionJun 26, 2024-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45505.png

Downloads & links

-
Map

FileDownload / File: emd_45505.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 427.008 Å		0.83 Å/pix.
x 512 pix.
= 427.008 Å		0.83 Å/pix.
x 512 pix.
= 427.008 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.447
Minimum - Maximum-1.2852708 - 2.6635067
Average (Standard dev.)0.006839285 (±0.11142456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 427.008 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_45505_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FljJM flagellar filament (asymmetrical)

EntireName: FljJM flagellar filament (asymmetrical)
Components
  • Complex: FljJM flagellar filament (asymmetrical)
    • Protein or peptide: Flagellin FljM

-
Supramolecule #1: FljJM flagellar filament (asymmetrical)

SupramoleculeName: FljJM flagellar filament (asymmetrical) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caulobacter vibrioides (bacteria) / Strain: NA1000

-
Macromolecule #1: Flagellin FljM

MacromoleculeName: Flagellin FljM / type: protein_or_peptide / ID: 1 / Number of copies: 38 / Enantiomer: LEVO
Source (natural)Organism: Caulobacter vibrioides (bacteria) / Strain: NA1000
Molecular weightTheoretical: 27.95024 KDa
SequenceString: MALNSINTNS GALIALQNLN STNAELTQVQ QRINTGKKIG SAKDNGAIWA TAKNQSATAG SMNAVKDSLQ RGQSTIDVAL AAGDTITDL LGKMKEKALA ASDTSLNTAS FNALKSDFDS LRDQITKAAS NAKFNGVSIA DGTTTKLSFL ANSDGSAFTV T AKTLTLGG ...String:
MALNSINTNS GALIALQNLN STNAELTQVQ QRINTGKKIG SAKDNGAIWA TAKNQSATAG SMNAVKDSLQ RGQSTIDVAL AAGDTITDL LGKMKEKALA ASDTSLNTAS FNALKSDFDS LRDQITKAAS NAKFNGVSIA DGTTTKLSFL ANSDGSAFTV T AKTLTLGG LGLTATSSFT TAAAAKTMIG TIDTALQTAT NKLASLGTSS TGLDTHLTFV GKLQDSLDAG VGNLVDADLA KE SAKLQSL QTKQQLGVQA LSIANQSSSS ILSLFR

UniProtKB: Flagellin FljM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER / Details: Featureless Cylinder
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 109957
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

1-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9ceo:
Caulobacter crescentus FljJM flagellar filament (asymmetrical)

+
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