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- EMDB-33797: Cryo-EM structure of the EfPiwi (N959K)-piRNA-target ternary complex -
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Open data
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Basic information
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Title | Cryo-EM structure of the EfPiwi (N959K)-piRNA-target ternary complex | |||||||||
![]() | overall map | |||||||||
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![]() | piRNA / Piwi protein / Argonaute / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | ![]() piRNA binding / regulatory ncRNA-mediated gene silencing / P granule / RNA endonuclease activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Li ZQ / Liu HB / Wu JP / Shen EZ | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 25.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.1 KB 19.1 KB | Display Display | ![]() |
Images | ![]() | 76.4 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() ![]() | 24.4 MB 25.1 MB 25.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yfqMC ![]() 7yfxC ![]() 7yfyC ![]() 7yg6C ![]() 7ygnC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | overall map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: DeepEMhancer processed map
File | emd_33797_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer processed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_33797_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_33797_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : EfPiwi(N959K)-piRNA-16nt target
Entire | Name: EfPiwi(N959K)-piRNA-16nt target |
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Components |
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-Supramolecule #1: EfPiwi(N959K)-piRNA-16nt target
Supramolecule | Name: EfPiwi(N959K)-piRNA-16nt target / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Supramolecule #2: EfPiwi(N959K)
Supramolecule | Name: EfPiwi(N959K) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: RNA
Supramolecule | Name: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2 |
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-Macromolecule #1: piRNA
Macromolecule | Name: piRNA / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.957792 KDa |
Sequence | String: UUACCAUCAA CAUGGAAACU UGGC(OMU) |
-Macromolecule #2: RNA (5'-R(*UP*CP*CP*AP*UP*GP*UP*UP*GP*AP*UP*GP*GP*UP*AP*A)-3')
Macromolecule | Name: RNA (5'-R(*UP*CP*CP*AP*UP*GP*UP*UP*GP*AP*UP*GP*GP*UP*AP*A)-3') type: rna / ID: 2 / Details: 16nt RNA target / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 5.100047 KDa |
Sequence | String: UCCAUGUUGA UGGUAA |
-Macromolecule #3: Piwi
Macromolecule | Name: Piwi / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 92.654094 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MDYKDDDDKG SDYKDDDDKG SDYKDDDDKG SENLYFQGSL NVESSMVSQR GSSGQPVPVS ANYLPLKGNM DGVFKYAVGF NPPVEDIRS RSQLLNEHKE LIGLTRVFDG STLYVPKRIC EQRLDLMSTR QTDGASIKVT ISLVDSVKNR DVVQLMNVIF K RILRSLKL ...String: MDYKDDDDKG SDYKDDDDKG SDYKDDDDKG SENLYFQGSL NVESSMVSQR GSSGQPVPVS ANYLPLKGNM DGVFKYAVGF NPPVEDIRS RSQLLNEHKE LIGLTRVFDG STLYVPKRIC EQRLDLMSTR QTDGASIKVT ISLVDSVKNR DVVQLMNVIF K RILRSLKL QRIGRDYYDA NSPLEVPQHK MQLWPGYVTA INRHEGGLML VLDVSHRVMK TDTALDFLYE LYHFNQDKFR EE AFKQLVG SVVLTRYNNR TYEIDDIAWD KNPRCAFQDH AGSQITFVDY YKRAYDLDIT DLEQPLLIHR PKKKQRGKQD EGR KEVEEM VCLVPELCAM TGLTDAARSD FKVMKDLAVH TRVPPEKRAE SFRKFIQRLN TTKEASELLH SWGLVLDSRM LDMQ GRRLP PEKILFKHSS IVANMEADWS RECLKEHVIS AVSLLDWAVL FVRKDQGKAT DFVNMLSKVC PPIGMEVHEP KMVEV VNDR TESYLRALRE LIAPRLQMVV IVFPTSRDDR YSAVKKLCCI ESPIPSQVLI ARTITQQQKL RSVAQKVALQ MNAKLG GEL WAVEIPLKSC MVVGIDVYHD KSYGNKSIAG FVASTNPSFT RWYSRTAMQE QSQELIHELK LCMQAALKKY NEMNQSL PE RIIVFRDGVG EGREEYVSEF EVPQFNSCFS IFGENYCPKL AVVVVQKRIT TRIFGRSGHS YDNPPPGVIV DHTITKSY D FYLVSQHVRQ GTVSPTYYRV IYDKSGLKPD HLQRLTYKLT HMYYNWPGTI RTPAPCKYAH KLAFLVGKSL HRDPAHELS DRLFFL UniProtKB: Piwi |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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 model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 221896 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |