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- EMDB-33817: Cryo-EM structure of the Mili in complex with piRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-33817
TitleCryo-EM structure of the Mili in complex with piRNA
Map dataoverall map
Sample
  • Complex: Mili-piRNA
    • Complex: Mili
      • Protein or peptide: Piwi-like protein 2
    • Complex: piRNA
      • RNA: piRNA
  • Ligand: MAGNESIUM ION
KeywordspiRNA / Piwi protein / Argonaute / RNA binding protein / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


perinucleolar chromocenter / piRNA-mediated gene silencing by mRNA destabilization / transposable element silencing by piRNA-mediated DNA methylation / PET complex / pi-body / secondary piRNA processing / transposable element silencing by mRNA destabilization / positive regulation of meiosis I / piRNA binding / transposable element silencing by heterochromatin formation ...perinucleolar chromocenter / piRNA-mediated gene silencing by mRNA destabilization / transposable element silencing by piRNA-mediated DNA methylation / PET complex / pi-body / secondary piRNA processing / transposable element silencing by mRNA destabilization / positive regulation of meiosis I / piRNA binding / transposable element silencing by heterochromatin formation / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / germ-line stem cell population maintenance / negative regulation of circadian rhythm / chromatoid body / dense body / positive regulation of cytoplasmic translation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / regulatory ncRNA-mediated gene silencing / P granule / oogenesis / RNA endonuclease activity / meiotic cell cycle / rhythmic process / spermatogenesis / mRNA binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain ...DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / 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 speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLi ZQ / Liu HB / Wu JP / Shen EZ
Funding support China, 1 items
OrganizationGrant numberCountry
Other privateWestlake Education Foundation (101486021901) China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Mammalian PIWI-piRNA-target complexes reveal features for broad and efficient target silencing.
Authors: Zhiqing Li / Zhenzhen Li / Yuqi Zhang / Lunni Zhou / Qikui Xu / Lili Li / Lin Zeng / Junchao Xue / Huilin Niu / Jing Zhong / Qilu Yu / Dengfeng Li / Miao Gui / Yongping Huang / Shikui Tu / ...Authors: Zhiqing Li / Zhenzhen Li / Yuqi Zhang / Lunni Zhou / Qikui Xu / Lili Li / Lin Zeng / Junchao Xue / Huilin Niu / Jing Zhong / Qilu Yu / Dengfeng Li / Miao Gui / Yongping Huang / Shikui Tu / Zhao Zhang / Chun-Qing Song / Jianping Wu / En-Zhi Shen /
Abstract: The PIWI-interacting RNA (piRNA) pathway is an adaptive defense system wherein piRNAs guide PIWI family Argonaute proteins to recognize and silence ever-evolving selfish genetic elements and ensure ...The PIWI-interacting RNA (piRNA) pathway is an adaptive defense system wherein piRNAs guide PIWI family Argonaute proteins to recognize and silence ever-evolving selfish genetic elements and ensure genome integrity. Driven by this intensive host-pathogen arms race, the piRNA pathway and its targeted transposons have coevolved rapidly in a species-specific manner, but how the piRNA pathway adapts specifically to target silencing in mammals remains elusive. Here, we show that mouse MILI and human HILI piRNA-induced silencing complexes (piRISCs) bind and cleave targets more efficiently than their invertebrate counterparts from the sponge Ephydatia fluviatilis. The inherent functional differences comport with structural features identified by cryo-EM studies of piRISCs. In the absence of target, MILI and HILI piRISCs adopt a wider nucleic-acid-binding channel and display an extended prearranged piRNA seed as compared with EfPiwi piRISC, consistent with their ability to capture targets more efficiently than EfPiwi piRISC. In the presence of target, the seed gate-which enforces seed-target fidelity in microRNA RISC-adopts a relaxed state in mammalian piRISC, revealing how MILI and HILI tolerate seed-target mismatches to broaden the target spectrum. A vertebrate-specific lysine distorts the piRNA seed, shifting the trajectory of the piRNA-target duplex out of the central cleft and toward the PAZ lobe. Functional analyses reveal that this lysine promotes target binding and cleavage. Our study therefore provides a molecular basis for the piRNA targeting mechanism in mice and humans, and suggests that mammalian piRNA machinery can achieve broad target silencing using a limited supply of piRNA species.
History
DepositionJul 11, 2022-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33817.png

Downloads & links

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Map

FileDownload / File: emd_33817.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationoverall map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 192 pix.
= 208.704 Å		1.09 Å/pix.
x 192 pix.
= 208.704 Å		1.09 Å/pix.
x 192 pix.
= 208.704 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.95
Minimum - Maximum-6.246632 - 8.5068035
Average (Standard dev.)-0.0006778375 (±0.19974442)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 208.70401 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhancer processed map

Fileemd_33817_additional_1.map
AnnotationDeepEMhancer processed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_33817_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_33817_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mili-piRNA

EntireName: Mili-piRNA
Components
  • Complex: Mili-piRNA
    • Complex: Mili
      • Protein or peptide: Piwi-like protein 2
    • Complex: piRNA
      • RNA: piRNA
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Mili-piRNA

SupramoleculeName: Mili-piRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Mili

SupramoleculeName: Mili / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: piRNA

SupramoleculeName: piRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: Piwi-like protein 2

MacromoleculeName: Piwi-like protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 91.850211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG SDYKDDDDKG SDYKDDDDKG SENLYFQGKE LLVKQGSKGT PQSLGLNLIK IQCHNEAVYQ YHVTFSPSVE CKSMRFGML KDHQSVTGNV TAFDGSILYL PVKLQQVVEL KSQRKTDDAE ISIKIQLTKI LEPCSDLCIP FYNVVFRRVM K LLDMKLVG ...String:
MDYKDDDDKG SDYKDDDDKG SDYKDDDDKG SENLYFQGKE LLVKQGSKGT PQSLGLNLIK IQCHNEAVYQ YHVTFSPSVE CKSMRFGML KDHQSVTGNV TAFDGSILYL PVKLQQVVEL KSQRKTDDAE ISIKIQLTKI LEPCSDLCIP FYNVVFRRVM K LLDMKLVG RNFYDPTSAM VLQQHRLQIW PGYAASIRRT DGGLFLLADV SHKVIRNDSV LDVMHAIYQQ NKEHFQDECS KL LVGSIVI TRYNNRTYRI DDVDWNKTPK DSFVMSDGKE ITFLEYYSKN YGITVKEDDQ PLLIHRPSER QNNHGMLLKG EIL LLPELS FMTGIPEKMK KDFRAMKDLT QQINLSPKQH HGALECLLQR ISQNETASNE LTRWGLSLHK DVHKIEGRLL PMER INLRN TSFVTSEDLN WVKEVTRDAS ILTIPMHFWA LFYPKRAMDQ ARELVNMLEK IAGPIGMRIS PPAWVELKDD RIETY IRTI QSLLGVEGKI QMVVCIIMGT RDDLYGAIKK LCCVQSPVPS QVINVRTIGQ PTRLRSVAQK ILLQMNCKLG GELWGV DIP LKQLMVIGMD VYHDPSRGMR SVVGFVASIN LTLTKWYSRV VFQMPHQEIV DSLKLCLVGS LKKYYEVNHC LPEKIVV YR DGVSDGQLKT VANYEIPQLQ KCFEAFDNYH PKMVVFVVQK KISTNLYLAA PDHFVTPSPG TVVDHTITSC EWVDFYLL A HHVRQGCGIP THYICVLNTA NLSPDHMQRL TFKLCHMYWN WPGTIRVPAP CKYAHKLAFL SGQILHHEPA IQLCGNLFF L

UniProtKB: Piwi-like protein 2

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Macromolecule #2: piRNA

MacromoleculeName: piRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.262972 KDa
SequenceString:
UUACCAUCAA CAUGGAAACU UGGCU(OMC)

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 673342
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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