[English] 日本語
Yorodumi
- EMDB-9974: Structure of Salmonella flagellar hook reveals intermolecular dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9974
TitleStructure of Salmonella flagellar hook reveals intermolecular domain interactions for the universal joint function
Map data
Sample
  • Complex: Flagellar hook
    • Protein or peptide: Flagellar hook protein FlgE
KeywordsFlgE / universal joint / axial structure / motor protein
Function / homology
Function and homology information


bacterial-type flagellum hook / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / cytosol
Similarity search - Function
Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal ...Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar hook protein FlgE / Flagellar hook protein FlgE
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsHorvath P / Kato T
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP25000013 Japan
Japan Society for the Promotion of Science18K06155 Japan
CitationJournal: Biomolecules / Year: 2019
Title: Structure ofSalmonellaFlagellar Hook Reveals Intermolecular Domain Interactions for the Universal Joint Function.
Authors: Horvath P / Kato T / Miyata T / Namba K
History
DepositionJul 8, 2019-
Header (metadata) releaseOct 16, 2019-
Map releaseOct 16, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6kfk
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6kfk
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

-
Map

FileDownload / File: emd_9974.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.085525736 - 0.14024903
Average (Standard dev.)0.00039747966 (±0.009452366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-196-196-392
Dimensions392392392
Spacing392392392
CellA=B=C: 321.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z392392392
origin x/y/z0.0000.0000.000
length x/y/z321.440321.440321.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-196-196-392
NC/NR/NS392392392
D min/max/mean-0.0860.1400.000

-
Supplemental data

-
Sample components

-
Entire : Flagellar hook

EntireName: Flagellar hook
Components
  • Complex: Flagellar hook
    • Protein or peptide: Flagellar hook protein FlgE

-
Supramolecule #1: Flagellar hook

SupramoleculeName: Flagellar hook / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 42 kDa/nm

-
Macromolecule #1: Flagellar hook protein FlgE

MacromoleculeName: Flagellar hook protein FlgE / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 42.101957 KDa
SequenceString: SFSQAVSGLN AAATNLDVIG NNIANSATYG FKSGTASFAD MFAGSKVGLG VKVAGITQDF TDGTTTNTGR GLDVAISQNG FFRLVDSNG SVFYSRNGQF KLDENRNLVN MQGMQLTGYP ATGTPPTIQQ GANPAPITIP NTLMAAKSTT TASMQINLNS T DPVPSKTP ...String:
SFSQAVSGLN AAATNLDVIG NNIANSATYG FKSGTASFAD MFAGSKVGLG VKVAGITQDF TDGTTTNTGR GLDVAISQNG FFRLVDSNG SVFYSRNGQF KLDENRNLVN MQGMQLTGYP ATGTPPTIQQ GANPAPITIP NTLMAAKSTT TASMQINLNS T DPVPSKTP FSVSDADSYN KKGTVTVYDS QGNAHDMNVY FVKTKDNEWA VYTHDSSDPA ATAPTTASTT LKFNENGILE SG GTVNITT GTINGATAAT FSLSFLNSMQ QNTGANNIVA TNQNGYKPGD LVSYQINNDG TVVGNYSNEQ EQVLGQIVLA NFA NNEGLA SQGDNVWAAT QASGVALLGT AGSGNFGKLT NGALEASNVD LSKELVNMIV AQRNYQSNAQ TIKTQDQILN TLVN LR

UniProtKB: Flagellar hook protein FlgE

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3TRIS
100.0 mMNaClSodium Chloride
GridModel: Quantifoil R0.6/1 / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 275.15 K

-
Electron microscopy

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Number real images: 486 / Average exposure time: 6.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal magnification: 50000
Sample stageCooling holder cryogen: NITROGEN

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.05 Å
Applied symmetry - Helical parameters - Δ&Phi: 64.78 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 41568
Segment selectionNumber selected: 42293
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2)

-
Atomic model buiding 1

Initial model
PDB IDChain

3a69

chain_id: A, residue_range: 1-402, source_name: PDB, initial_model_type: experimental model

5jxl

chain_id: A, residue_range: 28-46, source_name: PDB, initial_model_type: experimental model

5jxl

chain_id: A, residue_range: 65-92, source_name: PDB, initial_model_type: experimental model
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-6kfk:
Structure of Salmonella flagellar hook reveals intermolecular domain interactions for the universal joint function

+
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