2024-07-17 REL PDBe PDBe PDBe 2022-02-18 2022-11-16 2022-11-16 2024-07-17 Czech Science Foundation GA22-19896S Czech Republic Ministry of Education, Youth and Sports of the Czech Republic LM2018127 Czech Republic Mouse endoribonuclease Dicer (composite structure) Zanova M Zapletal D Kubicek K Stefl R Pinkas M Novacek J endoribonuclease, gene silencing, post-transcriptional, catalytic enzyme, cytoplasm, RNA BINDING PROTEIN Zapletal D Taborska E Pasulka J Malik R Kubicek K Zanova M Much C Sebesta M Buccheri V Horvat F Jenickova I Prochazkova M Prochazka J Pinkas M Novacek J Joseph DF Sedlacek R Bernecky C O'Carroll D Stefl R Svoboda P Structural and functional basis of mammalian microRNA biogenesis by Dicer. Mol.Cell US 82 4064 4079.e13 2022 36332606 doi:10.1016/j.molcel.2022.10.010 1097-2765 2168 MOCEFL EMD-14383 other EM volume
EMD-14383 contains the same protein complexed with pre-miR-15a
 EMD-14384 other EM volume
EMD-14384 contains oocyte isoform of the same protein complexed with pre-miR-15a
 EMD-15297 other EM volume
Consensus map
 EMD-15298 other EM volume
Focused refinement
 EMD-15299 other EM volume
Focused refinement
 7yz4 FULLOVERLAP Free form of mouse somatic dicer Free form of mouse somatic dicer 0 1 Mus musculus Endoribonuclease Dicer Mus musculus 0.226809594 1 Baculovirus expression vector pFastBac1-HM LEVO MVWSHPQFEKGGGSGGGSGGSAWSHPQFEKGDYPYDVPDYAGTENLYFQGLVDMKSPALQPLSMAGLQLMTPASSPMGPF FGLPWQQEAIHDNIYTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELAHQIRGDLNPHAKRTVFLVNSANQVA QQVSAVRTHSDLKVGEYSDLEVNASWTKERWSQEFTKHQVLIMTCYVALTVLKNGYLSLSDINLLVFDECHLAILDHPYR EIMKLCESCPSCPRILGLTASILNGKCDPEELEEKIQKLERILRSDAETATDLVVLDRYTSQPCEIVVDCGPFTDRSGLY ERLLMELEAALDFINDCNVAVHSKERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELHRKFLLF TDTLLRKIHALCEEYFSPASLDLKYVTPKVMKLLEILRKYKPYERQQFESVEWYNNRNQDNYVSWSDSEDDDDDEEIEEK EKPETNFPSPFTNILCGIIFVERRYTAVVLNRLIKEAGKQDPELAYISSNFITGHGIGKNQPRSKQMEAEFRKQEEVLRK FRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRARAPISNYVMLADTDKIKSFEEDLKTYKAIEKILR NKCSKSADGAEADVHAGVDDEDAFPPYVLRPDDGGPRVTINTAIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTL YLPINSPLRASIVGPPMDSVRLAERVVALICCEKLHKIGELDEHLMPVGKETVKYEEELDLHDEEETSVPGRPGSTKRRQ CYPKAIPECLRESYPKPDQPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTI SIELKKSGFTLSQQMLELITRLHQYIFSHILRLEKPALEFKPTGAESAYCVLPLNVVNDSGTLDIDFKFMEDIEKSEARI GIPSTKYSKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPL LDVDHTSSRLNLLTPRHLNQKGKALPLSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLLTA EELRAQTASDAGVGVRSLPVDFRYPNLDFGWKKSIDSKSFISSCNSSLAESDNYCKHSTTVVPEHAAHQGATRPSLENHD QMSVNCKRLPAESPAKLQSEVSTDLTAINGLSYNKNLANGSYDLVNRDFCQGNQLNYFKQEIPVQPTTSYPIQNLYNYEN QPKPSNECPLLSNTYLDGNANTSTSDGSPAVSTMPAMMNAVKALKDRMDSEQSPSVGYSSRTLGPNPGLILQALTLSNAS DGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDPPVNWLPPGYVV NQDKSNSEKWEKDEMTKDCLLANGKLGEACEEEEDLTWRAPKEEAEDEDDFLEYDQEHIQFIDSMLMGSGAFVRKISLSP FSASDSAYEWKMPKKASLGSMPFASGLEDFDYSSWDAMCYLDPSKAVEEDDFVVGFWNPSEENCGVDTGKQSISYDLHTE QCIADKSIADCVAALLGCYLTSCGERAAQLFLCSLGLKVLPVIKRTSREKALDPAQENGSSQQKSLSGSCASPVGPRSSA GKDLEYGCLKIPPRCMFDHPDAEKTLNHLISGFETFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILD YLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEMQGMDSELRRSE EDEEKEEDIEVPKAMGDIFASLAGAIYMDSGMSLEVVWQVYYPMMQPLIEKFSANVPRSPVRELLEMEPETAKFSPAERT YDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLKANQPQVPNSGRGENLYFQGASDYKDHDGDYKDHDGSHHHH HHHH Q8R418 3.1.26.3 singleParticle particle 0.20 8.0 50.0 Tris 100.0 Sodium Chloride 1.0 Dithiotreitol 2.0 Magensium Chloride
The buffer was always prepared fresh
 ETHANE 100 277.15 FEI VITROBOT MARK IV
Described in STAR methods.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 3.5 GATAN K2 SUMMIT (4k x 4k) COUNTING 6354 55.0 1 862842 81 FOURIER SPACE 3.84 FSC 0.143 CUT-OFF cryoSPARC v3.3.1
The map resolution was further improved up to 3.47 with local refinement of the individual protein domains.
92906 NOT APPLICABLE NOT APPLICABLE 100 1377.0 cryoSPARC v3.3.1 emd_14387.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 317.952 317.952 317.952 90.0 90.0 90.0 X Y Z -0.79996276 7.68432 0.0018962272 0.047948804 0.828 0.828 0.828 0.103 AUTHOR combined map from the locally refined parts of the protein FLEXIBLE FIT
Endoribonuclease mouse Dicer from AlphaFold database was used as initial model. Initial local fitting into combined map from locally refined protein parts was done using Chimera and then Coot's Real Space Refine Zone.
Ramachandran Plot, Rotamer Analysis, Density Analysis REAL 87.799999999999997 FLEXIBLE FIT
PHENIX Real-space refinement was used for flexible fitting.
Correlation coefficient REAL 87.799999999999997 FLEXIBLE FIT
ISOLDE was used for flexible fitting with defined torsion restraints
Ramachandran Plot, Rotamer Analysis, Clash Score REAL 87.799999999999997 emd_14387_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 317.952 317.952 317.952 90.0 90.0 90.0 X Y Z -0.15526111 0.3932753 0.000200609 0.011618332 0.828 0.828 0.828 AUTHOR EM map of the whole protein, before local refinement emd_14387_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 317.952 317.952 317.952 90.0 90.0 90.0 X Y Z -0.0017190247 3.8909564 0.000424258 0.014933476 0.828 0.828 0.828 AUTHOR locally refined part of the protein emd_14387_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 317.952 317.952 317.952 90.0 90.0 90.0 X Y Z -0.0017785085 2.5332315 0.0005049407 0.01705039 0.828 0.828 0.828 AUTHOR locally refined part of the protein emd_14387_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 317.952 317.952 317.952 90.0 90.0 90.0 X Y Z -0.7156421 0.6609823 0.00027881598 0.071909286 0.828 0.828 0.828 AUTHOR half map A emd_14387_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 317.952 317.952 317.952 90.0 90.0 90.0 X Y Z -0.6695688 0.7010797 0.00026855254 0.07182388 0.828 0.828 0.828 AUTHOR half map B