[English] 日本語
Yorodumi
- PDB-9cef: Caulobacter crescentus FljN flagellar filament (symmetrized) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cef
TitleCaulobacter crescentus FljN flagellar filament (symmetrized)
ComponentsFlagellin FljN
KeywordsSTRUCTURAL PROTEIN / flagellin / flagellar filament
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 FljN
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.22 Å
AuthorsSanchez, J.C. / Montemayor, E.J. / Ploscariu, N.T. / Parrell, D. / Baumgardt, J.K. / Yang, J.E. / Sibert, B. / Cai, K. / Wright, E.R.
Funding support United States, 5items
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, J.C. / Montemayor, E.J. / Ploscariu, N.T. / Parrell, D. / Baumgardt, J.K. / Yang, J.E. / Sibert, B. / Cai, K. / Wright, E.R.
History
DepositionJun 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellin FljN
B: Flagellin FljN
C: Flagellin FljN
D: Flagellin FljN
E: Flagellin FljN
F: Flagellin FljN
G: Flagellin FljN
H: Flagellin FljN
I: Flagellin FljN
J: Flagellin FljN
K: Flagellin FljN
L: Flagellin FljN
M: Flagellin FljN
N: Flagellin FljN
O: Flagellin FljN
P: Flagellin FljN
Q: Flagellin FljN
R: Flagellin FljN
S: Flagellin FljN
T: Flagellin FljN
U: Flagellin FljN
V: Flagellin FljN
W: Flagellin FljN
X: Flagellin FljN
Y: Flagellin FljN
Z: Flagellin FljN
a: Flagellin FljN
b: Flagellin FljN
c: Flagellin FljN
d: Flagellin FljN
e: Flagellin FljN
f: Flagellin FljN
g: Flagellin FljN
h: Flagellin FljN
i: Flagellin FljN
j: Flagellin FljN
k: Flagellin FljN
l: Flagellin FljN
m: Flagellin FljN
n: Flagellin FljN
o: Flagellin FljN
p: Flagellin FljN
q: Flagellin FljN
r: Flagellin FljN


Theoretical massNumber of molelcules
Total (without water)1,229,76744
Polymers1,229,76744
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
Flagellin FljN


Mass: 27949.256 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Source: (natural) Caulobacter vibrioides (bacteria) / Strain: NA1000 / References: UniProt: O52530

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: FljN flagellar filament (symmetrized) / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.28 kDa/nm / Experimental value: NO
Source (natural)Organism: Caulobacter vibrioides (bacteria) / Strain: NA1000
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / C2 aperture diameter: 70 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
13cryoSPARC4.43D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 65.923 ° / Axial rise/subunit: 4.778 Å / Axial symmetry: C1
3D reconstructionResolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131070 / Symmetry type: HELICAL
Atomic model buildingB value: 67 / Space: REAL
Atomic model buildingAccession code: AF-O52530-F1 / Source name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00885668
ELECTRON MICROSCOPYf_angle_d0.686115984
ELECTRON MICROSCOPYf_dihedral_angle_d4.28512012
ELECTRON MICROSCOPYf_chiral_restr0.0514960
ELECTRON MICROSCOPYf_plane_restr0.00514828

+
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://pdbjlvh1.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