[English] 日本語
Yorodumi
- PDB-9u4r: Structure of the intial complex in filament assembly at 3.23 angs... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9u4r
TitleStructure of the intial complex in filament assembly at 3.23 angstroms resolution, conformation 2.
Components
  • (Flagellar hook-associated protein 2) x 2
  • Flagellar hook protein FlgE
  • Flagellar hook-associated protein 1
  • Flagellar hook-associated protein 3
KeywordsPROTEIN FIBRIL / flagellum / filament assembly / intial complex / fibril
Function / homology
Function and homology information


bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / cell adhesion / structural molecule activity / extracellular region / cytosol
Similarity search - Function
: / Flagellar hook-associated protein 1, D2-like domain / Flagellar hook-associated protein 1 / : / Flagellar hook-associated protein FlgK helical domain / Flagellar hook-associated protein 3 / Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus ...: / Flagellar hook-associated protein 1, D2-like domain / Flagellar hook-associated protein 1 / : / Flagellar hook-associated protein FlgK helical domain / Flagellar hook-associated protein 3 / Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin hook, IN motif / Flagellin hook IN motif / 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 / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Flagellar hook protein FlgE / Flagellar hook-associated protein 1 / Flagellar hook-associated protein 3 / Flagellar hook-associated protein 2
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsChen, L.X. / Jiang, W.X. / Cheng, X.Q. / Dong, X. / Xing, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371277 China
National Natural Science Foundation of China (NSFC)32301028 China
CitationJournal: To Be Published
Title: Structure of the intial complex in filament assembly at 3.23 angstroms resolution, conformation 2.
Authors: Chen, L.X. / Jiang, W.X. / Cheng, X.Q. / Dong, X. / Xing, Q.
History
DepositionMar 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: Flagellar hook-associated protein 2
AB: Flagellar hook-associated protein 2
AC: Flagellar hook-associated protein 2
AD: Flagellar hook-associated protein 2
AE: Flagellar hook-associated protein 2
BA: Flagellar hook-associated protein 3
BB: Flagellar hook-associated protein 3
BC: Flagellar hook-associated protein 3
BD: Flagellar hook-associated protein 3
BE: Flagellar hook-associated protein 3
BG: Flagellar hook-associated protein 3
BH: Flagellar hook-associated protein 3
BI: Flagellar hook-associated protein 3
BJ: Flagellar hook-associated protein 3
BK: Flagellar hook-associated protein 3
BL: Flagellar hook-associated protein 3
BM: Flagellar hook-associated protein 3
BN: Flagellar hook-associated protein 3
CA: Flagellar hook-associated protein 1
CB: Flagellar hook-associated protein 1
CC: Flagellar hook-associated protein 1
CD: Flagellar hook-associated protein 1
CE: Flagellar hook-associated protein 1
CF: Flagellar hook-associated protein 1
CG: Flagellar hook-associated protein 1
CH: Flagellar hook-associated protein 1
CI: Flagellar hook-associated protein 1
CJ: Flagellar hook-associated protein 1
CK: Flagellar hook-associated protein 1
DA: Flagellar hook protein FlgE
DB: Flagellar hook protein FlgE
DC: Flagellar hook protein FlgE
DD: Flagellar hook protein FlgE
DE: Flagellar hook protein FlgE
DF: Flagellar hook protein FlgE
DG: Flagellar hook protein FlgE
DH: Flagellar hook protein FlgE
DI: Flagellar hook protein FlgE
DJ: Flagellar hook protein FlgE
DK: Flagellar hook protein FlgE
EA: Flagellar hook protein FlgE
EB: Flagellar hook protein FlgE
EC: Flagellar hook protein FlgE
ED: Flagellar hook protein FlgE
EE: Flagellar hook protein FlgE
EF: Flagellar hook protein FlgE
EG: Flagellar hook protein FlgE
EH: Flagellar hook protein FlgE
EI: Flagellar hook protein FlgE
EJ: Flagellar hook protein FlgE
EK: Flagellar hook protein FlgE
FA: Flagellar hook protein FlgE
FB: Flagellar hook protein FlgE
FC: Flagellar hook protein FlgE
FD: Flagellar hook protein FlgE
FE: Flagellar hook protein FlgE
FF: Flagellar hook protein FlgE
FG: Flagellar hook protein FlgE
FH: Flagellar hook protein FlgE
FI: Flagellar hook protein FlgE
FJ: Flagellar hook protein FlgE
FK: Flagellar hook protein FlgE
GA: Flagellar hook protein FlgE
GB: Flagellar hook protein FlgE
GC: Flagellar hook protein FlgE
GD: Flagellar hook protein FlgE
GE: Flagellar hook protein FlgE
GF: Flagellar hook protein FlgE
GG: Flagellar hook protein FlgE
GH: Flagellar hook protein FlgE
GI: Flagellar hook protein FlgE
GJ: Flagellar hook protein FlgE
GK: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)3,202,99873
Polymers3,202,99873
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Flagellar hook-associated protein 2 / FliD1 / HAP2 / Filament cap protein / Flagellar cap protein


Mass: 49887.594 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P16328
#2: Protein Flagellar hook-associated protein 2 / FliD3 / HAP2 / Filament cap protein / Flagellar cap protein


Mass: 49871.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P16328
#3: Protein
Flagellar hook-associated protein 3 / HAP3 / Hook-filament junction protein


Mass: 34201.965 Da / Num. of mol.: 13 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P16326
#4: Protein
Flagellar hook-associated protein 1 / HAP1


Mass: 59153.781 Da / Num. of mol.: 11 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1J5
#5: Protein ...
Flagellar hook protein FlgE


Mass: 42233.152 Da / Num. of mol.: 44 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1J1
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Intial complex in filament assembly / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254124 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 224.33 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002221962
ELECTRON MICROSCOPYf_angle_d0.4545301828
ELECTRON MICROSCOPYf_chiral_restr0.03735616
ELECTRON MICROSCOPYf_plane_restr0.00340301
ELECTRON MICROSCOPYf_dihedral_angle_d3.9430937

+
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