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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | dsRNA transporter | |||||||||
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![]() | dsRNA transporter / ![]() | |||||||||
Function / homology | ![]() RNA transmembrane transporter activity / dsRNA transport / RNA transport / regulatory ncRNA-mediated post-transcriptional gene silencing / ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Jiang DH / Zhang JT | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into double-stranded RNA recognition and transport by SID-1. Authors: Jiangtao Zhang / Chunhua Zhan / Junping Fan / Dian Wu / Ruixue Zhang / Di Wu / Xinyao Chen / Ying Lu / Ming Li / Min Lin / Jianke Gong / Daohua Jiang / ![]() Abstract: RNA uptake by cells is critical for RNA-mediated gene interference (RNAi) and RNA-based therapeutics. In Caenorhabditis elegans, RNAi is systemic as a result of SID-1-mediated double-stranded RNA ...RNA uptake by cells is critical for RNA-mediated gene interference (RNAi) and RNA-based therapeutics. In Caenorhabditis elegans, RNAi is systemic as a result of SID-1-mediated double-stranded RNA (dsRNA) across cells. Despite the functional importance, the underlying mechanisms of dsRNA internalization by SID-1 remain elusive. Here we describe cryogenic electron microscopy structures of SID-1, SID-1-dsRNA complex and human SID-1 homologs SIDT1 and SIDT2, elucidating the structural basis of dsRNA recognition and import by SID-1. The homodimeric SID-1 homologs share conserved architecture, but only SID-1 possesses the molecular determinants within its extracellular domains for distinguishing dsRNA from single-stranded RNA and DNA. We show that the removal of the long intracellular loop between transmembrane helix 1 and 2 attenuates dsRNA uptake and systemic RNAi in vivo, suggesting a possible endocytic mechanism of SID-1-mediated dsRNA internalization. Our study provides mechanistic insights into dsRNA internalization by SID-1, which may facilitate the development of dsRNA applications based on SID-1. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.3 KB 15.3 KB | Display Display | ![]() |
Images | ![]() | 76.5 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hkeMC ![]() 8hipC ![]() 8j6mC ![]() 8j6oC 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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Map
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34850_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34850_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : dsRNA transporter
Entire | Name: dsRNA transporter |
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Components |
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-Supramolecule #1: dsRNA transporter
Supramolecule | Name: dsRNA transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Systemic RNA interference defective protein 1
Macromolecule | Name: Systemic RNA interference defective protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 88.02757 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MIRVYLIILM HLVIGLTQNN STTPSPIITS SNSSVLVFEI SSKMKMIEKK LEANTVHVLR LELDQSFILD LTKVAAEIVD SSKYSKEDG VILEVTVSNG RDSFLLKLPT VYPNLKLYTD GKLLNPLVEQ DFGAHRKRHR IGDPHFHQNL IVTVQSRLNA D IDYRLHVT ...String: MIRVYLIILM HLVIGLTQNN STTPSPIITS SNSSVLVFEI SSKMKMIEKK LEANTVHVLR LELDQSFILD LTKVAAEIVD SSKYSKEDG VILEVTVSNG RDSFLLKLPT VYPNLKLYTD GKLLNPLVEQ DFGAHRKRHR IGDPHFHQNL IVTVQSRLNA D IDYRLHVT HLDRAQYDFL KFKTGQTTKT LSNQKLTFVK PIGFFLNCSE QNISQFHVTL YSEDDICANL ITVPANESIY DR SVISDKT HNRRVLSFTK RADIFFTETE ISMFKSFRIF VFIAPDDSGC STNTSRKSFN EKKKISFEFK KLENQSYAVP TAL MMIFLT TPCLLFLPIV INIIKNSRKL APSQSNLISF SPVPSEQRDM DLSHDEQQNT SSELENNGEI PAAENQIVEE ITAE NQETS VEEGNREIQV KIPLKQDSLS LHGQMLQYPV AIILPVLMHT AIEFHKWTTS TMANRDEMCF HNHACARPLG ELRAW NNII TNIGYTLYGA IFIVLSICRR GRHEYSHVFG TYECTLLDVT IGVFMVLQSI ASATYHICPS DVAFQFDTPC IQVICG LLM VRQWFVRHES PSPAYTNILL VGVVSLNFLI SAFSKTSYVR FIIAVIHVIV VGSICLAKER SLGSEKLKTR FFIMAFS MG NFAAIVMYLT LSAFHLNQIA TYCFIINCIM YLMYYGCMKV LHSERITSKA KLCGALSLLA WAVAGFFFFQ DDTDWTRS A AASRALNKPC LLLGFFGSHD LWHIFGALAG LFTFIFVSFV DDDLINTRKT SINIF UniProtKB: Systemic RNA interference defective protein 1 |
-Macromolecule #2: RNA (37-MER)
Macromolecule | Name: RNA (37-MER) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.894137 KDa |
Sequence | String: GGGCAAUGUG ACUGCAUCAG CAGUCACAUU GCCCAAG |
-Macromolecule #3: RNA (37-MER)
Macromolecule | Name: RNA (37-MER) / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.825017 KDa |
Sequence | String: CUUGGGCAAU GUGACUGCUG AUGCAGUCAC AUUGCCC |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108090 |