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- EMDB-60610: Cryo-EM Structure of EfPiwi-piRNA-target (25-nt, comma) -

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Basic information

Entry
Database: EMDB / ID: EMD-60610
TitleCryo-EM Structure of EfPiwi-piRNA-target (25-nt, comma)
Map data
Sample
  • Complex: EfPiwi-piRNA-target (25-nt, comma)
    • Protein or peptide: Piwi
    • RNA: RNA (25-MER)
    • RNA: RNA (5'-R(P*AP*GP*CP*CP*AP*AP*GP*UP*UP*UP*CP*CP*AP*UP*GP*UP*UP*GP*AP*UP*GP*GP*UP*A)-3')
KeywordsPiwi protein / Pi-RNA / Argonaute / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


Piwi, N-terminal domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain ...Piwi, N-terminal domain / 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
Biological speciesHomo sapiens (human) / Ephydatia fluviatilis (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLi ZQ / Xu QK / Wu JP / Shen EZ
Funding support1 items
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, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60610.png

Downloads & links

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Map

FileDownload / File: emd_60610.map.gz / Format: CCP4 / Size: 19.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 172 pix.
= 173.273 Å		1.01 Å/pix.
x 172 pix.
= 173.273 Å		1.01 Å/pix.
x 172 pix.
= 173.273 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.074
Minimum - Maximum-0.25734377 - 0.56335986
Average (Standard dev.)-0.0004071917 (±0.015246023)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions172172172
Spacing172172172
CellA=B=C: 173.27281 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60610_half_map_1.map
Projections & Slices
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Slices (1/2)
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Half map: #2

Fileemd_60610_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : EfPiwi-piRNA-target (25-nt, comma)

EntireName: EfPiwi-piRNA-target (25-nt, comma)
Components
  • Complex: EfPiwi-piRNA-target (25-nt, comma)
    • Protein or peptide: Piwi
    • RNA: RNA (25-MER)
    • RNA: RNA (5'-R(P*AP*GP*CP*CP*AP*AP*GP*UP*UP*UP*CP*CP*AP*UP*GP*UP*UP*GP*AP*UP*GP*GP*UP*A)-3')

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Supramolecule #1: EfPiwi-piRNA-target (25-nt, comma)

SupramoleculeName: EfPiwi-piRNA-target (25-nt, comma) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Piwi

MacromoleculeName: Piwi / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ephydatia fluviatilis (invertebrata)
Molecular weightTheoretical: 110.611969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGRGGRGAA LLKALEQPVR RPGQQPVQSG DQVAGPPSLT SATVSTVGVV QQHTVADVDR CPPLATPASG QPLTLHRPLG SPAVLPLGG RGGRGSRSVE PVEPRVASEP PSLISFGPSS PERAHTETEI TPPTAVSVQQ RPSSQTISRG VPAVGRGSML R DPTSHVRL ...String:
MSGRGGRGAA LLKALEQPVR RPGQQPVQSG DQVAGPPSLT SATVSTVGVV QQHTVADVDR CPPLATPASG QPLTLHRPLG SPAVLPLGG RGGRGSRSVE PVEPRVASEP PSLISFGPSS PERAHTETEI TPPTAVSVQQ RPSSQTISRG VPAVGRGSML R DPTSHVRL PQLYSSGGSP VVQTATATPT VSPPALSPSP PLLTQSPPSQ SPLPIKAIKD LSLNVESSMV SQRGSSGQPV PV SANYLPL KGNMDGVFKY AVGFNPPVED IRSRSQLLNE HKELIGLTRV FDGSTLYVPK RICEQRLDLM STRQTDGASI KVT ISLVDS VKNRDVVQLM NVIFKRILRS LKLQRIGRDY YDANSPLEVP QHKMQLWPGY VTAINRHEGG LMLVLDVSHR VMKT DTALD FLYELYHFNQ DKFREEAFKQ LVGSVVLTRY NNRTYEIDDI AWDKNPRCAF QDHAGSQITF VDYYKRAYDL DITDL EQPL LIHRPKKKQR GKQDEGRKEV EEMVCLVPEL CAMTGLTDAA RSDFKVMKDL AVHTRVPPEK RAESFRKFIQ RLNTTK EAS ELLHSWGLVL DSRMLDMQGR RLPPEKILFK HSSIVANMEA DWSRECLKEH VISAVSLLDW AVLFVRKDQG KATDFVN ML SKVCPPIGME VHEPKMVEVV NDRTESYLRA LRELIAPRLQ MVVIVFPTSR DDRYSAVKKL CCIESPIPSQ VLIARTIT Q QQKLRSVAQK VALQMNAKLG GELWAVEIPL KSCMVVGIDV YHDKSYGNKS IAGFVASTNP SFTRWYSRTA MQEQSQELI HELKLCMQAA LKKYNEMNQS LPERIIVFRD GVGEGREEYV SEFEVPQFNS CFSIFGENYC PKLAVVVVQK RITTRIFGRS GHSYDNPPP GVIVDHTITK SYDFYLVSQH VRQGTVSPTY YRVIYDKSGL KPDHLQRLTY KLTHMYYNWP GTIRTPAPCN Y AHKLAFLV GKSLHRDPAH ELSDRLFFL

UniProtKB: Piwi

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Macromolecule #2: RNA (25-MER)

MacromoleculeName: RNA (25-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.943764 KDa
SequenceString:
UUACCAUCAA CAUGGAAACU UGGCU

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Macromolecule #3: RNA (5'-R(P*AP*GP*CP*CP*AP*AP*GP*UP*UP*UP*CP*CP*AP*UP*GP*UP*UP*GP...

MacromoleculeName: RNA (5'-R(P*AP*GP*CP*CP*AP*AP*GP*UP*UP*UP*CP*CP*AP*UP*GP*UP*UP*GP*AP*UP*GP*GP*UP*A)-3')
type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.671567 KDa
SequenceString:
AGCCAAGUUU CCAUGUUGAU GGUA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67583
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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