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- EMDB-21051: Human Drosha and DGCR8 in complex with Primary MicroRNA (MP/RNA c... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21051 | |||||||||||||||
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Title | Human Drosha and DGCR8 in complex with Primary MicroRNA (MP/RNA complex) - Active state | |||||||||||||||
![]() | Human Drosha and DGCR8 in complex with Primary MicroRNA (MP/RNA complex) - Active state | |||||||||||||||
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![]() | Microprocessor / Drosha / DGCR8 / Primary MicroRNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||||||||
Function / homology | ![]() positive regulation of pre-miRNA processing / regulation of miRNA metabolic process / protein-RNA adaptor activity / primary miRNA binding / DEAD/H-box RNA helicase binding / regulation of regulatory T cell differentiation / U4 snRNA 3'-end processing / Transcriptional Regulation by MECP2 / ribonuclease III / miRNA metabolic process ...positive regulation of pre-miRNA processing / regulation of miRNA metabolic process / protein-RNA adaptor activity / primary miRNA binding / DEAD/H-box RNA helicase binding / regulation of regulatory T cell differentiation / U4 snRNA 3'-end processing / Transcriptional Regulation by MECP2 / ribonuclease III / miRNA metabolic process / primary miRNA processing / regulation of stem cell proliferation / ribonuclease III activity / microprocessor complex / pre-miRNA processing / MicroRNA (miRNA) biogenesis / termination of RNA polymerase II transcription / SMAD binding / R-SMAD binding / lipopolysaccharide binding / rRNA processing / double-stranded RNA binding / protein-macromolecule adaptor activity / site of double-strand break / regulation of inflammatory response / defense response to Gram-negative bacterium / postsynaptic density / nuclear body / defense response to Gram-positive bacterium / glutamatergic synapse / DNA damage response / heme binding / positive regulation of gene expression / nucleolus / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
![]() | Partin A / Zhang K | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA. Authors: Alexander C Partin / Kaiming Zhang / Byung-Cheon Jeong / Emily Herrell / Shanshan Li / Wah Chiu / Yunsun Nam / ![]() Abstract: Metazoan microRNAs require specific maturation steps initiated by Microprocessor, comprising Drosha and DGCR8. Lack of structural information for the assembled complex has hindered an understanding ...Metazoan microRNAs require specific maturation steps initiated by Microprocessor, comprising Drosha and DGCR8. Lack of structural information for the assembled complex has hindered an understanding of how Microprocessor recognizes primary microRNA transcripts (pri-miRNAs). Here we present a cryoelectron microscopy structure of human Microprocessor with a pri-miRNA docked in the active site, poised for cleavage. The basal junction is recognized by a four-way intramolecular junction in Drosha, triggered by the Belt and Wedge regions that clamp over the ssRNA. The belt is important for efficiency and accuracy of pri-miRNA processing. Two dsRBDs form a molecular ruler to measure the stem length between the two dsRNA-ssRNA junctions. The specific organization of the dsRBDs near the apical junction is independent of Drosha core domains, as observed in a second structure in the partially docked state. Collectively, we derive a molecular model to explain how Microprocessor recognizes a pri-miRNA and accurately identifies the cleavage site. | |||||||||||||||
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 | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.9 KB 17.9 KB | Display Display | ![]() |
Images | ![]() | 150 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 488.8 KB | Display | ![]() |
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Full document | ![]() | 488.3 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v5bMC ![]() 6v5cC 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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Annotation | Human Drosha and DGCR8 in complex with Primary MicroRNA (MP/RNA complex) - Active state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 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 : Human Drosha and DGCR8 in complex with Primary MicroRNA (MP/RNA c...
Entire | Name: Human Drosha and DGCR8 in complex with Primary MicroRNA (MP/RNA complex) - Active state |
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Components |
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-Supramolecule #1: Human Drosha and DGCR8 in complex with Primary MicroRNA (MP/RNA c...
Supramolecule | Name: Human Drosha and DGCR8 in complex with Primary MicroRNA (MP/RNA complex) - Active state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40 KDa |
-Macromolecule #1: Ribonuclease 3
Macromolecule | Name: Ribonuclease 3 / 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: 118.379727 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GSGHRSPSRE KKRARWEEEK DRWSDNQSSG KDKNYTSIKE KEPEETMPDK NEEEEEELLK PVWIRCTHSE NYYSSDPMDQ VGDSTVVGT SRLRDLYDKF EEELGSRQEK AKAARPPWEP PKTKLDEDLE SSSESECESD EDSTCSSSSD SEVFDVIAEI K RKKAHPDR ...String: GSGHRSPSRE KKRARWEEEK DRWSDNQSSG KDKNYTSIKE KEPEETMPDK NEEEEEELLK PVWIRCTHSE NYYSSDPMDQ VGDSTVVGT SRLRDLYDKF EEELGSRQEK AKAARPPWEP PKTKLDEDLE SSSESECESD EDSTCSSSSD SEVFDVIAEI K RKKAHPDR LHDELWYNDP GQMNDGPLCK CSAKARRTGI RHSIYPGEEA IKPCRPMTNN AGRLFHYRIT VSPPTNFLTD RP TVIEYDD HEYIFEGFSM FAHAPLTNIP LCKVIRFNID YTIHFIEEMM PENFCVKGLE LFSLFLFRDI LELYDWNLKG PLF EDSPPC CPRFHFMPRF VRFLPDGGKE VLSMHQILLY LLRCSKALVP EEEIANMLQW EELEWQKYAE ECKGMIVTNP GTKP SSVRI DQLDREQFNP DVITFPIIVH FGIRPAQLSY AGDPQYQKLW KSYVKLRHLL ANSPKVKQTD KQKLAQREEA LQKIR QKNT MRREVTVELS SQGFWKTGIR SDVCQHAMML PVLTHHIRYH QCLMHLDKLI GYTFQDRCLL QLAMTHPSHH LNFGMN PDH ARNSLSNCGI RQPKYGDRKV HHMHMRKKGI NTLINIMSRL GQDDPTPSRI NHNERLEFLG DAVVEFLTSV HLYYLFP SL EEGGLATYRT AIVQNQHLAM LAKKLELDRF MLYAHGPDLC RESDLRHAMA NCFEALIGAV YLEGSLEEAK QLFGRLLF N DPDLREVWLN YPLHPLQLQE PNTDRQLIET SPVLQKLTEF EEAIGVIFTH VRLLARAFTL RTVGFNHLTL GHNQRMEFL GDSIMQLVAT EYLFIHFPDH HEGHLTLLRS SLVNNRTQAK VAEELGMQEY AITNDKTKRP VALRTKTLAD LLESFIAALY IDKDLEYVH TFMNVCFFPR LKEFILNQDW NDPKSQLQQC CLTLRTEGKE PDIPLYKTLQ TVGPSHARTY TVAVYFKGER I GCGKGPSI QQAEMGAAMD ALEKYNFPQM AHQKRFIERK YRQELKEMRW EREHQERE UniProtKB: Ribonuclease 3 |
-Macromolecule #2: Microprocessor complex subunit DGCR8
Macromolecule | Name: Microprocessor complex subunit DGCR8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 60.550602 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSGAIVQRDR VDEEALNFPY EDDFDNDVDA LLEEGLCAPK KRRTEEKYGG DSDHPSDGET SVQPMMTKIK TVLKSRGRPP TEPLPDGWI MTFHNSGVPV YLHRESRVVT WSRPYFLGTG SIRKHDPPLS SIPCLHYKKM KDNEEREQSS DLTPSGDVSP V KPLSRSAE ...String: GSGAIVQRDR VDEEALNFPY EDDFDNDVDA LLEEGLCAPK KRRTEEKYGG DSDHPSDGET SVQPMMTKIK TVLKSRGRPP TEPLPDGWI MTFHNSGVPV YLHRESRVVT WSRPYFLGTG SIRKHDPPLS SIPCLHYKKM KDNEEREQSS DLTPSGDVSP V KPLSRSAE LEFPLDEPDS MGADPGPPDE KDPLGAEAAP GALGQVKAKV EVCKDESVDL EEFRSYLEKR FDFEQVTVKK FR TWAERRQ FNREMKRKQA ESERPILPAN QKLITLSVQD APTKKEFVIN PNGKSEVCIL HEYMQRVLKV RPVYNFFECE NPS EPFGAS VTIDGVTYGS GTASSKKLAK NKAARATLEI LIPDFVKQTS EEKPKDSEEL EYFNHISIED SRVYELTSKA GLLS PYQIL HECLKRNHGM GDTSIKFEVV PGKNQKSEYV MACGKHTVRG WCKNKRVGKQ LASQKILQLL HPHVKNWGSL LRMYG RESS KMVKQETSDK SVIELQQYAK KNKPNLHILS KLQEEMKRLA EEREETRK UniProtKB: Microprocessor complex subunit DGCR8 |
-Macromolecule #3: Pri-miR-16-2 (78-MER)
Macromolecule | Name: Pri-miR-16-2 (78-MER) / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 33.646934 KDa |
Sequence | String: CUGACAUACU UGUUCCACUC UAGCAGCACG UAAAUAUUGG CGUAGUGAAA UAUAUAUUAA ACACCAAUAU UACUGUGCUG CUUUAGUGU GACAGGGAUA CAGCAA GENBANK: GENBANK: AC024221.23 |
-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 |
-Macromolecule #5: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4.2 mg/mL |
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Buffer | pH: 7.1 |
Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 35 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
Details | Human Drosha and DGCR8 in complex with Primary MicroRNA (MP/RNA complex) - Active state |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-30 / Number grids imaged: 8 / Number real images: 12681 / Average exposure time: 6.0 sec. / Average electron dose: 46.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
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Output model | ![]() PDB-6v5b: |