[English] 日本語
Yorodumi
- PDB-9myg: Cryo-EM structure of Natrinema sp. J7-2 Type IV pilus, PilA1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9myg
TitleCryo-EM structure of Natrinema sp. J7-2 Type IV pilus, PilA1
ComponentsArchaeal Type IV pilin N-terminal domain-containing protein
KeywordsPROTEIN FIBRIL / Type IV pilus / Pilin / Biofilm
Function / homology:
Function and homology information
Biological speciesNatrinema sp. J7-2 (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 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: Cell Rep / Year: 2025
Title: A type IV pili-mediated mutualism between two co-resident temperate archaeal viruses and their host.
Authors: Jialin Xiang / Ravi R Sonani / Yangyang Wang / Zhao Chen / Weiyan Xiong / Jiangling Chen / Shuyu Li / Kang An / Yixuan Wang / Ying Liu / Mark A B Kreutzberger / Mart Krupovic / Edward H ...Authors: Jialin Xiang / Ravi R Sonani / Yangyang Wang / Zhao Chen / Weiyan Xiong / Jiangling Chen / Shuyu Li / Kang An / Yixuan Wang / Ying Liu / Mark A B Kreutzberger / Mart Krupovic / Edward H Egelman / Shishen Du / Xiangdong Chen /
Abstract: Co-resident temperate viruses are ubiquitous in prokaryotes, which interact with each other and affect their shared host. However, how such virus-virus and virus-host interactions play out in Archaea ...Co-resident temperate viruses are ubiquitous in prokaryotes, which interact with each other and affect their shared host. However, how such virus-virus and virus-host interactions play out in Archaea remains largely unexplored. Here, we discover a tripartite mutualistic interaction among the co-existing temperate viruses SNJ1 and SNJ2 and their host, haloarchaeon Natrinema sp. J7. We find that the SNJ2 provirus encodes two type IV pilins (T4Ps), which hijack the host secretion machinery to assemble into distinct filaments on the host cell surface. The SNJ2-encoded pili are dispensable for the SNJ2 infection but serve as receptors for SNJ1. As a quid pro quo, SNJ1 enhances the replication of SNJ2. Furthermore, the viral pili are the dominant filaments on the cell surface and promote biofilm formation and motility of the host. A number of SNJ2-like proviruses harbor T4P genes, suggesting that T4P-mediated virus-virus and virus-host interactions are widespread in Haloarchaea.
History
DepositionJan 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Archaeal Type IV pilin N-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)15,6161
Polymers15,6161
Non-polymers00
Water00
1
A: Archaeal Type IV pilin N-terminal domain-containing protein
x 24


Theoretical massNumber of molelcules
Total (without water)374,78824
Polymers374,78824
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation23
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 24 / Rise per n subunits: 4.95 Å / Rotation per n subunits: 108.81 °)

-
Components

#1: Protein Archaeal Type IV pilin N-terminal domain-containing protein


Mass: 15616.163 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Natrinema sp. J7-2 (archaea) / Gene: NJ7G_0728 / Production host: Natrinema sp. J7-2 (archaea) / References: UniProt: I7CEX0
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Type IV pilus / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Natrinema sp. J7-2 (archaea)
Source (recombinant)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: 1400 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: 108.81 ° / Axial rise/subunit: 4.95 Å / Axial symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35647 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002959
ELECTRON MICROSCOPYf_angle_d0.5081308
ELECTRON MICROSCOPYf_dihedral_angle_d3.491137
ELECTRON MICROSCOPYf_chiral_restr0.046169
ELECTRON MICROSCOPYf_plane_restr0.001171

+
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