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- EMDB-6905: Cryo-EM structure of human Dicer and its complexes with a pre-miR... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6905 | |||||||||
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Title | Cryo-EM structure of human Dicer and its complexes with a pre-miRNA substrate | |||||||||
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Function / homology | ![]() regulation of siRNA processing / regulation of miRNA processing / regulation of viral transcription / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / regulation of regulatory ncRNA processing / peripheral nervous system myelin formation / negative regulation of defense response to virus by host / pre-miRNA binding / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / global gene silencing by mRNA cleavage ...regulation of siRNA processing / regulation of miRNA processing / regulation of viral transcription / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / regulation of regulatory ncRNA processing / peripheral nervous system myelin formation / negative regulation of defense response to virus by host / pre-miRNA binding / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / global gene silencing by mRNA cleavage / Small interfering RNA (siRNA) biogenesis / tRNA decay / negative regulation of Schwann cell proliferation / ribonuclease III / positive regulation of myelination / apoptotic DNA fragmentation / deoxyribonuclease I activity / nerve development / positive regulation of Schwann cell differentiation / RISC-loading complex / miRNA metabolic process / RISC complex assembly / ribonuclease III activity / miRNA processing / pre-miRNA processing / siRNA binding / siRNA processing / Regulation of MITF-M-dependent genes involved in apoptosis / M-decay: degradation of maternal mRNAs by maternally stored factors / pre-mRNA binding / RISC complex / MicroRNA (miRNA) biogenesis / miRNA binding / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of viral genome replication / protein sequestering activity / RNA endonuclease activity / neuron projection morphogenesis / helicase activity / negative regulation of protein kinase activity / PKR-mediated signaling / double-stranded RNA binding / regulation of translation / nuclear body / protein domain specific binding / negative regulation of gene expression / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
![]() | Liu Z / Wang J / Cheng H / Ke X / Sun L / Zhang QC / Wang H-W | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate. Authors: Zhongmin Liu / Jia Wang / Hang Cheng / Xin Ke / Lei Sun / Qiangfeng Cliff Zhang / Hong-Wei Wang / ![]() Abstract: Human Dicer (hDicer) is a multi-domain protein belonging to the RNase III family. It plays pivotal roles in small RNA biogenesis during the RNA interference (RNAi) pathway by processing a diverse ...Human Dicer (hDicer) is a multi-domain protein belonging to the RNase III family. It plays pivotal roles in small RNA biogenesis during the RNA interference (RNAi) pathway by processing a diverse range of double-stranded RNA (dsRNA) precursors to generate ∼22 nt microRNA (miRNA) or small interfering RNA (siRNA) products for sequence-directed gene silencing. In this work, we solved the cryoelectron microscopy (cryo-EM) structure of hDicer in complex with its cofactor protein TRBP and revealed the precise spatial arrangement of hDicer's multiple domains. We further solved structures of the hDicer-TRBP complex bound with pre-let-7 RNA in two distinct conformations. In combination with biochemical analysis, these structures reveal a property of the hDicer-TRBP complex to promote the stability of pre-miRNA's stem duplex in a pre-dicing state. These results provide insights into the mechanism of RNA processing by hDicer and illustrate the regulatory role of hDicer's N-terminal helicase domain. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.4 KB 19.4 KB | Display Display | ![]() |
Images | ![]() | 63.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zalMC ![]() 6904C ![]() 6906C ![]() 5zakC ![]() 5zamC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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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Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Dicer and trbp
Entire | Name: Dicer and trbp |
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Components |
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-Supramolecule #1: Dicer and trbp
Supramolecule | Name: Dicer and trbp / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 270 KDa |
-Supramolecule #2: Human Dicer-TRBP with Pre-let-7 complex Class I
Supramolecule | Name: Human Dicer-TRBP with Pre-let-7 complex Class I / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Endoribonuclease Dicer
Macromolecule | Name: Endoribonuclease Dicer / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease III |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 218.947328 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MKSPALQPLS MAGLQLMTPA SSPMGPFFGL PWQQEAIHDN IYTPRKYQVE LLEAALDHNT IVCLNTGSGK TFIAVLLTKE LSYQIRGDF SRNGKRTVFL VNSANQVAQQ VSAVRTHSDL KVGEYSNLEV NASWTKERWN QEFTKHQVLI MTCYVALNVL K NGYLSLSD ...String: MKSPALQPLS MAGLQLMTPA SSPMGPFFGL PWQQEAIHDN IYTPRKYQVE LLEAALDHNT IVCLNTGSGK TFIAVLLTKE LSYQIRGDF SRNGKRTVFL VNSANQVAQQ VSAVRTHSDL KVGEYSNLEV NASWTKERWN QEFTKHQVLI MTCYVALNVL K NGYLSLSD INLLVFDECH LAILDHPYRE IMKLCENCPS CPRILGLTAS ILNGKCDPEE LEEKIQKLEK ILKSNAETAT DL VVLDRYT SQPCEIVVDC GPFTDRSGLY ERLLMELEEA LNFINDCNIS VHSKERDSTL ISKQILSDCR AVLVVLGPWC ADK VAGMMV RELQKYIKHE QEELHRKFLL FTDTFLRKIH ALCEEHFSPA SLDLKFVTPK VIKLLEILRK YKPYERQQFE SVEW YNNRN QDNYVSWSDS EDDDEDEEIE EKEKPETNFP SPFTNILCGI IFVERRYTAV VLNRLIKEAG KQDPELAYIS SNFIT GHGI GKNQPRNKQM EAEFRKQEEV LRKFRAHETN LLIATSIVEE GVDIPKCNLV VRFDLPTEYR SYVQSKGRAR APISNY IML ADTDKIKSFE EDLKTYKAIE KILRNKCSKS VDTGETDIDP VMDDDDVFPP YVLRPDDGGP RVTINTAIGH INRYCAR LP SDPFTHLAPK CRTRELPDGT FYSTLYLPIN SPLRASIVGP PMSCVRLAER VVALICCEKL HKIGELDDHL MPVGKETV K YEEELDLHDE EETSVPGRPG STKRRQCYPK AIPECLRDSY PRPDQPCYLY VIGMVLTTPL PDELNFRRRK LYPPEDTTR CFGILTAKPI PQIPHFPVYT RSGEVTISIE LKKSGFMLSL QMLELITRLH QYIFSHILRL EKPALEFKPT DADSAYCVLP LNVVNDSST LDIDFKFMED IEKSEARIGI PSTKYTKETP FVFKLEDYQD AVIIPRYRNF DQPHRFYVAD VYTDLTPLSK F PSPEYETF AEYYKTKYNL DLTNLNQPLL DVDHTSSRLN LLTPRHLNQK GKALPLSSAE KRKAKWESLQ NKQILVPELC AI HPIPASL WRKAVCLPSI LYRLHCLLTA EELRAQTASD AGVGVRSLPA DFRYPNLDFG WKKSIDSKSF ISISNSSSAE NDN YCKHST IVPENAAHQG ANRTSSLENH DQMSVNCRTL LSESPGKLHV EVSADLTAIN GLSYNQNLAN GSYDLANRDF CQGN QLNYY KQEIPVQPTT SYSIQNLYSY ENQPQPSDEC TLLSNKYLDG NANKSTSDGS PVMAVMPGTT DTIQVLKGRM DSEQS PSIG YSSRTLGPNP GLILQALTLS NASDGFNLER LEMLGDSFLK HAITTYLFCT YPDAHEGRLS YMRSKKVSNC NLYRLG KKK GLPSRMVVSI FDPPVNWLPP GYVVNQDKSN TDKWEKDEMT KDCMLANGKL DEDYEEEDEE EESLMWRAPK EEADYED DF LEYDQEHIRF IDNMLMGSGA FVKKISLSPF STTDSAYEWK MPKKSSLGSM PFSSDFEDFD YSSWDAMCYL DPSKAVEE D DFVVGFWNPS EENCGVDTGK QSISYDLHTE QCIADKSIAD CVEALLGCYL TSCGERAAQL FLCSLGLKVL PVIKRTDRE KALCPTRENF NSQQKNLSVS CAAASVASSR SSVLKDSEYG CLKIPPRCMF DHPDADKTLN HLISGFENFE KKINYRFKNK AYLLQAFTH ASYHYNTITD CYQRLEFLGD AILDYLITKH LYEDPRQHSP GVLTDLRSAL VNNTIFASLA VKYDYHKYFK A VSPELFHV IDDFVQFQLE KNEMQGMDSE LRRSEEDEEK EEDIEVPKAM GDIFESLAGA IYMDSGMSLE TVWQVYYPMM RP LIEKFSA NVPRSPVREL LEMEPETAKF SPAERTYDGK VRVTVEVVGK GKFKGVGRSY RIAKSAAARR ALRSLKANQP QVP NS |
-Macromolecule #2: RISC-loading complex subunit TARBP2
Macromolecule | Name: RISC-loading complex subunit TARBP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 39.085277 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSEEEQGSGT TTGCGLPSIE QMLAANPGKT PISLLQEYGT RIGKTPVYDL LKAEGQAHQP NFTFRVTVGD TSCTGQGPSK KAAKHKAAE VALKHLKGGS MLEPALEDSS SFSPLDSSLP EDIPVFTAAA AATPVPSVVL TRSPPMELQP PVSPQQSECN P VGALQELV ...String: MSEEEQGSGT TTGCGLPSIE QMLAANPGKT PISLLQEYGT RIGKTPVYDL LKAEGQAHQP NFTFRVTVGD TSCTGQGPSK KAAKHKAAE VALKHLKGGS MLEPALEDSS SFSPLDSSLP EDIPVFTAAA AATPVPSVVL TRSPPMELQP PVSPQQSECN P VGALQELV VQKGWRLPEY TVTQESGPAH RKEFTMTCRV ERFIEIGSGT SKKLAKRNAA AKMLLRVHTV PLDARDGNEV EP DDDHFSI GVGSRLDGLR NRGPGCTWDS LRNSVGEKIL SLRSCSLGSL GALGPACCRV LSELSEEQAF HVSYLDIEEL SLS GLCQCL VELSTQPATV CHGSATTREA ARGEAARRAL QYLKIMAGSK |
-Macromolecule #3: RNA (73-mer)
Macromolecule | Name: RNA (73-mer) / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.37583 KDa |
Sequence | String: UGAGGUAGUA GGUUGUAUAG UUUUAGGGUC ACACCCACCA CUGGGAGAUA ACUAUACAAU CUACUGUCUU ACC |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 Details: 50 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM DTT, 2 mM CaCl2 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Details: The grid was glow-discharged prior to use. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
Details | This sample was mono-disperse. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.0 K / Max: 80.0 K |
Specialist optics | Phase plate: OTHER |
Details | no |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 2849 / Average exposure time: 5.44 sec. / Average electron dose: 50.0 e/Å2 / Details: no |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 2.5 µm / Calibrated magnification: 36496 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 89000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |