[English] 日本語
Yorodumi
- PDB-9p0a: Structure of Natrinema sp. J7-2 Tafi pilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9p0a
TitleStructure of Natrinema sp. J7-2 Tafi pilus
ComponentsPilin
KeywordsPROTEIN FIBRIL / Extrcellular filament / Bundling pili
Function / homologyTwin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Uncharacterized protein
Function and homology information
Biological speciesNatrinema sp. J7-2 (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSonani, R.R. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Tat-dependent bundling pilus of a halophilic archaeon assembles by a strand donation mechanism and facilitates biofilm formation.
Authors: Ravi R Sonani / Ying Liu / Jialin Xiang / Virginija Cvirkaite-Krupovic / Shishen Du / Xiangdong Chen / Mart Krupovic / Edward H Egelman /
Abstract: Diverse extracellular filaments present on the surface of archaea mediate multiple key processes, such as motility, adhesion, and biofilm formation. Although several archaeal filament types have been ...Diverse extracellular filaments present on the surface of archaea mediate multiple key processes, such as motility, adhesion, and biofilm formation. Although several archaeal filament types have been characterized in considerable detail, many remain understudied, particularly those utilizing noncanonical secretion systems. Here, we describe the Tafi bundling pilus that facilitates biofilm formation in the haloarchaeon sp. J7-2. Unlike previously characterized archaeal pili, Tafi is secreted via the twin-arginine translocation (Tat) pathway, which transports fully folded proteins across the cytoplasmic membrane. Structural analysis reveals that although Tafi pili assemble via a canonical strand-donation mechanism, the pilin subunit (TafE) adopts a distinct structural topology that sets it apart from the previously characterized Sec-dependent pilins that form bundling pili in archaea. Sequence analyses show that TafE homologs are also present in thermophilic archaea from different phyla, but Tat-signal sequences are exclusive to pilins of halophilic archaea. Nevertheless, we find that Tat signal peptides in haloarchaeal TafE-like pili were exchanged back to the Sec signal peptides on multiple independent occasions. These findings expand our understanding of the diversity and evolution of archaeal extracellular filaments and highlight the Tat pathway as a route for pilus assembly in halophilic archaea.
History
DepositionJun 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Pilin
D: Pilin
E: Pilin


Theoretical massNumber of molelcules
Total (without water)65,0863
Polymers65,0863
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 Pilin


Mass: 21695.195 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Natrinema sp. J7-2 (archaea) / References: UniProt: I7CYY9
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Tafi pilus / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Natrinema sp. J7-2 (archaea)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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 defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -80.21 ° / Axial rise/subunit: 33.36 Å / Axial symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: OTHER / Num. of particles: 36787 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044083
ELECTRON MICROSCOPYf_angle_d0.6945583
ELECTRON MICROSCOPYf_dihedral_angle_d7.885585
ELECTRON MICROSCOPYf_chiral_restr0.047681
ELECTRON MICROSCOPYf_plane_restr0.006756

+
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