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- PDB-9iiy: Cryo-EM Structure of EfPiwi-piRNA-target (25-nt, bilobed) -

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Basic information

Entry
Database: PDB / ID: 9iiy
TitleCryo-EM Structure of EfPiwi-piRNA-target (25-nt, bilobed)
Components
  • Piwi
  • RNA (5'-R(P*CP*GP*UP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*GP*AP*UP*CP*AP*GP*CP*U)-3')
  • RNA (5'-R(P*UP*AP*GP*CP*AP*GP*AP*UP*CP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*AP*CP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / Piwi protein / Pi-RNA / Argonaute / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulatory ncRNA-mediated gene silencing / RNA binding / cytoplasm
Similarity search - Function
Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Piwi
Similarity search - Component
Biological speciesEphydatia fluviatilis (invertebrata)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLi, Z.Q. / Xu, Q.K. / Wu, J.P. / Shen, E.Z.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nature / Year: 2025
Title: Structural insights into RNA cleavage by PIWI Argonaute.
Authors: Zhiqing Li / Qikui Xu / Jing Zhong / Yan Zhang / Tianxiang Zhang / Xiaoze Ying / Xiaoli Lu / Xiaoyi Li / Li Wan / Junchao Xue / Jing Huang / Ying Zhen / Zhao Zhang / Jianping Wu / En-Zhi Shen /
Abstract: Argonaute proteins are categorized into AGO and PIWI clades. Across most animal species, AGO-clade proteins are widely expressed in various cell types, and regulate normal gene expression. By ...Argonaute proteins are categorized into AGO and PIWI clades. Across most animal species, AGO-clade proteins are widely expressed in various cell types, and regulate normal gene expression. By contrast, PIWI-clade proteins predominantly function during gametogenesis to suppress transposons and ensure fertility. Both clades use nucleic acid guides for target recognition by means of base pairing, crucial for initiating target silencing, often through direct cleavage. AGO-clade proteins use a narrow channel to secure a tight guide-target interaction. By contrast, PIWI proteins feature a wider channel that potentially allows mismatches during pairing, broadening target silencing capability. However, the mechanism of PIWI-mediated target cleavage remains unclear. Here we demonstrate that after target binding, PIWI proteins undergo a conformational change from an 'open' state to a 'locked' state, facilitating base pairing and enhancing target cleavage efficiency. This transition involves narrowing of the binding channel and repositioning of the PIWI-interacting RNA-target duplex towards the MID-PIWI lobe, establishing extensive contacts for duplex stabilization. During this transition, we also identify an intermediate 'comma-shaped' conformation, which might recruit GTSF1, a known auxiliary protein that enhances PIWI cleavage activity. GTSF1 facilitates the transition to the locked state by linking the PIWI domain to the RNA duplex, thereby expediting the conformational change critical for efficient target cleavage. These findings explain the molecular mechanisms underlying PIWI-PIWI-interacting RNA complex function in target RNA cleavage, providing insights into how dynamic conformational changes from PIWI proteins coordinate cofactors to safeguard gametogenesis.
History
DepositionJun 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_DOI / _citation.year / _em_admin.last_update
Revision 1.2Jan 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.3Mar 19, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Piwi
B: RNA (5'-R(P*UP*AP*GP*CP*AP*GP*AP*UP*CP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*AP*CP*G)-3')
C: RNA (5'-R(P*CP*GP*UP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*GP*AP*UP*CP*AP*GP*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)124,3443
Polymers124,3443
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Piwi


Mass: 110611.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ephydatia fluviatilis (invertebrata) / Gene: EfPiwiA / Production host: Homo sapiens (human) / References: UniProt: D5MRY8
#2: RNA chain RNA (5'-R(P*UP*AP*GP*CP*AP*GP*AP*UP*CP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*AP*CP*G)-3')


Mass: 7099.259 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: RNA chain RNA (5'-R(P*CP*GP*UP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*GP*AP*UP*CP*AP*GP*CP*U)-3')


Mass: 6632.997 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: EfPiwi-piRNA-target (25-nt, bilobed) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Ephydatia fluviatilis (invertebrata)31330
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87581 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026154
ELECTRON MICROSCOPYf_angle_d0.7758526
ELECTRON MICROSCOPYf_dihedral_angle_d14.5151195
ELECTRON MICROSCOPYf_chiral_restr0.075993
ELECTRON MICROSCOPYf_plane_restr0.005926

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