+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33800 | |||||||||
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Title | Cryo-EM structure of Hili in complex with piRNA | |||||||||
Map data | Hili with piRNA | |||||||||
Sample |
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Keywords | piRNA / Piwi protein / Argonaute / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information siRNA-mediated retrotransposon silencing by heterochromatin formation / perinucleolar chromocenter / retrotransposon silencing by mRNA destabilization / PET complex / pi-body / secondary piRNA processing / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / : / retrotransposon silencing by heterochromatin formation ...siRNA-mediated retrotransposon silencing by heterochromatin formation / perinucleolar chromocenter / retrotransposon silencing by mRNA destabilization / PET complex / pi-body / secondary piRNA processing / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / : / retrotransposon silencing by heterochromatin formation / positive regulation of meiosis I / germ-line stem cell population maintenance / negative regulation of circadian rhythm / chromatoid body / dense body / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / P granule / oogenesis / PIWI-interacting RNA (piRNA) biogenesis / RNA endonuclease activity / meiotic cell cycle / positive regulation of translation / rhythmic process / spermatogenesis / mRNA binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Li ZQ / Liu HB / Wu JP / Shen EZ | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33800.map.gz | 28.8 MB | EMDB map data format | |
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Header (meta data) | emd-33800-v30.xml emd-33800.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_33800.png | 108.4 KB | ||
Filedesc metadata | emd-33800.cif.gz | 6.2 KB | ||
Others | emd_33800_additional_1.map.gz emd_33800_half_map_1.map.gz emd_33800_half_map_2.map.gz | 28.7 MB 28.3 MB 28.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33800 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33800 | HTTPS FTP |
-Related structure data
Related structure data | 7yfxMC 7yfqC 7yfyC 7yg6C 7ygnC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33800.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Hili with piRNA | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.0773 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Overall map
File | emd_33800_additional_1.map | ||||||||||||
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Annotation | Overall map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_33800_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_33800_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hili-piRNA
Entire | Name: Hili-piRNA |
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Components |
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-Supramolecule #1: Hili-piRNA
Supramolecule | Name: Hili-piRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: Hili
Supramolecule | Name: Hili / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: piRNA
Supramolecule | Name: piRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: Piwi-like protein 2
Macromolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 114.404227 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDYKDDDDKG SDYKDDDDKG SDYKDDDDKG SENLYFQGMD PFRPSFRGQS PIHPSQCQAV RMPGCWPQAS KPLDPALGRG APAGRGHVF GKPEEPSTQR GPAQRESVGL VSMFRGLGIE TVSKTPLKRE MLPSGRGILG RGLSANLVRK DREELSPTFW D PKVLAAGD ...String: MDYKDDDDKG SDYKDDDDKG SDYKDDDDKG SENLYFQGMD PFRPSFRGQS PIHPSQCQAV RMPGCWPQAS KPLDPALGRG APAGRGHVF GKPEEPSTQR GPAQRESVGL VSMFRGLGIE TVSKTPLKRE MLPSGRGILG RGLSANLVRK DREELSPTFW D PKVLAAGD SKMAETSVGW SRTLGRGSSD ASLLPLGRAA GGISREVDKP PCTFSTPSRG PPQLSSPPAL PQSPLHSPDR PL VLTVEHK EKELIVKQGS KGTPQSLGLN LVKIQCHNEA VYQYHVTFSP NVECKSMRFG MLKDHQAVTG NVTAFDGSIL YLP VKLQQV LELKSQRKTD SAEISIKIQM TKILEPCSDL CIPFYNVVFR RVMKLLDMKL VGRNFYDPTS AMVLQQHRLQ IWPG YAASI RRTDGGLFLL ADVSHKVIRN DCVLDVMHAI YQQNKEHFQD ECTKLLVGNI VITRYNNRTY RIDDVDWNKT PKDSF TMSD GKEITFLEYY SKNYGITVKE EDQPLLIHRP SERQDNHGML LKGEILLLPE LSFMTGIPEK MKKDFRAMKD LAQQIN LSP KQHHSALECL LQRIAKNEAA TNELMRWGLR LQKDVHKIEG RVLPMERINL KNTSFITSQE LNWVKEVTRD PSILTIP MH FWALFYPKRA MDQARELVNM LEKIAGPIGM RMSPPAWVEL KDDRIETYVR TIQSTLGAEG KIQMVVCIIM GPRDDLYG A IKKLCCVQSP VPSQVVNVRT IGQPTRLRSV AQKILLQINC KLGGELWGVD IPLKQLMVIG MDVYHDPSRG MRSVVGFVA SINLTLTKWY SRVVFQMPHQ EIVDSLKLCL VGSLKKFYEV NHCLPEKIVV YRDGVSDGQL KTVANYEIPQ LQKCFEAFEN YQPKMVVFV VQKKISTNLY LAAPQNFVTP TPGTVVDHTI TSCEWVDFYL LAHHVRQGCG IPTHYVCVLN TANLSPDHMQ R LTFKLCHM YWNWPGTIRV PAPCKYAHKL AFLSGHILHH EPAIQLCENL FFL UniProtKB: Piwi-like protein 2 |
-Macromolecule #2: piRNA
Macromolecule | Name: piRNA / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.262972 KDa |
Sequence | String: UUACCAUCAA CAUGGAAACU UGGCU(OMC) |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70272 |