[English] 日本語
Yorodumi
- PDB-9v66: Structure of the Argonaute protein from Verrucomicrobia bacterium... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9v66
TitleStructure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA
Components
  • DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T)-3')
  • VbAgo
KeywordsRNA BINDING PROTEIN/DNA / mesophilic prokaryotic Argonaute / RNA BINDING PROTEIN-DNA complex
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesVerrucomicrobiota bacterium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsWu, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)240801001003 China
CitationJournal: Nat Commun / Year: 2026
Title: Structural insights into C-terminus-mediated RNA target cleavage by a mesophilic prokaryotic argonaute.
Authors: Taiyu Chen / Xin Tao / Shunshun Li / Qingmiao Duanmu / Jiening Wang / Kai Chen / Kangle Mu / Hong Yang / Yu Li / Yang Liu / Lixin Ma / Shan Wu /
Abstract: Prokaryotic Argonaute proteins (pAgos) are programmable nucleases that always utilize DNA guides to cleave DNA targets. Recent studies show that some pAgos preferentially utilize DNA guides to cleave ...Prokaryotic Argonaute proteins (pAgos) are programmable nucleases that always utilize DNA guides to cleave DNA targets. Recent studies show that some pAgos preferentially utilize DNA guides to cleave RNA targets rather than DNA targets. VbAgo, derived from a Verrucomicrobia bacterium, is a nuclease capable of specifically cleaving single-stranded RNA and highly structured RNA substrates at 37 °C, making it an ideal candidate for developing RNA manipulation toolkits. An in-depth investigation of its mechanism contributes to understanding the functional characteristics of gDtR-type Ago proteins. Here, we present cryo-electron microscopy structures of VbAgo, the VbAgo-guide DNA binary complex, multiple wild-type VbAgo-guide DNA-target RNA ternary complexes, and the catalytically inactive mutant (VbAgo-DM) guide DNA-target RNA ternary complex, with resolutions ranging from 2.5 to 3.2 Å. By integrating these cryo-EM structures with biochemical data, we elucidate the entire catalytic process of VbAgo, revealing its unique C-terminal regulatory mechanism. Specifically, in its apo state, VbAgo's C-terminus occupies the nucleic acid binding channel, partially impeding its catalytic activity while enhancing its stability. The binding of guide DNA displaces the C-terminus, and subsequent binding of target RNA, along with conformational changes in the N-terminal and PAZ domains, facilitates VbAgo dimerization. Following this, the C-terminus transitions from a loop to a helix, enabling maturation of the catalytic center and inducing movements in the MID-PIWI' interactions at the dimer interfaces, ultimately leading to dimer dissociation. Concurrently, cleavage of the target RNA and subsequent product release occur, after which VbAgo reverts to its binary state to initiate the next cleavage cycle. Moreover, we demonstrate that VbAgo exhibits guide DNA mediated RNA knockdown activity in mammalian cells. In summary, our study provides a comprehensive understanding of the molecular mechanisms governing self-inhibition, guide binding, target recognition, and product release in VbAgo. These findings offer valuable insights into the diverse mechanisms of pAgos, broadening their functional scope and enhancing the biotechnological potential of pAgo proteins.
History
DepositionMay 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 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
A: VbAgo
B: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1293
Polymers94,1052
Non-polymers241
Water1448
1


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

-
Components

#1: Protein VbAgo


Mass: 88463.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verrucomicrobiota bacterium (bacteria) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T)-3')


Mass: 5641.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verrucomicrobiota bacterium (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: VbAgo / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Verrucomicrobiota bacterium (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 186978 / Symmetry type: POINT
RefinementHighest resolution: 2.95 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026625
ELECTRON MICROSCOPYf_angle_d0.4089073
ELECTRON MICROSCOPYf_dihedral_angle_d14.5191030
ELECTRON MICROSCOPYf_chiral_restr0.038997
ELECTRON MICROSCOPYf_plane_restr0.0041127

+
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