2024-07-24 REL PDBe PDBe PDBe 2022-04-27 2022-12-28 2022-12-28 2024-07-24 Czech Science Foundation GA22-19896S Czech Republic Ministry of Education, Youth and Sports of the Czech Republic LM2018127 Czech Republic Mammalian Dicer in the "pre-dicing state" with pre-miR-15a substrate and TARBP2 subunit Zanova M Zapletal D Kubicek K Stefl R Pinkas M Novacek J endoribonuclease, dsRNA, complex, gene silencing, post-transcriptional, catalytic complex, cytoplasm, RISC-loading complex, TARBP2 RNA BINDING PROTEIN, 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-14384 other EM volume
14384 represents mouse oocyte Dicer in the "dicing state" with pre-miR-15a substrate
 EMD-14387 other EM volume
14387 contains same mouse somatic endoribonuclease Dicer
 EMD-14383 other EM volume
14383 contains same mouse somatic Dicer in the "pre-dicing state" with pre-miR-15a substrate
 7zpj FULLOVERLAP Pre-dicing state of mouse somatic dicer with pre-mir-15a and TARBP2 Pre-dicing state of mouse somatic dicer with pre-mir-15a and TARBP2 0 1 2 3 Pre-dicing state of mouse somatic dicer with TARBP2 1 1 3 Mus musculus Pre-mir-15a 1 2 Mus musculus Endoribonuclease Dicer Mus musculus 0.22692565599999998 1 Trichoplusia ni LEVO MVWSHPQFEKGGGSGGGSGGSAWSHPQFEKGDYPYDVPDYAGTENLYFQGLVDMKSPALQPLSMAGLQLMTPASSPMGPF FGLPWQQEAIHDNIYTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELAHQIRGDLNPHAKRTVFLVNSANQVA QQVSAVRTHSDLKVGEYSDLEVNASWTKERWSQEFTKHQVLIMTCYVALTVLKNGYLSLSDINLLVFDECHLAILDHPYR EIMKLCESCPSCPRILGLTASILNGKCDPEELEEKIQKLERILRSDAETATDLVVLDRYTSQPCEIVVDCGPFTDRSGLY ERLLMELEAALDFINDCNVAVHSKERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELHRKFLLF TDTLLRKIHALCEEYFSPASLDLKYVTPKVMKLLEILRKYKPYERQQFESVEWYNNRNQDNYVSWSDSEDDDDDEEIEEK EKPETNFPSPFTNILCGIIFVERRYTAVVLNRLIKEAGKQDPELAYISSNFITGHGIGKNQPRSKQMEAEFRKQEEVLRK FRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRARAPISNYVMLADTDKIKSFEEDLKTYKAIEKILR NKCSKSADGAEADVHAGVDDEDAFPPYVLRPDDGGPRVTINTAIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTL YLPINSPLRASIVGPPMDSVRLAERVVALICCEKLHKIGELDEHLMPVGKETVKYEEELDLHDEEETSVPGRPGSTKRRQ CYPKAIPECLRESYPKPDQPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTI SIELKKSGFTLSQQMLELITRLHQYIFSHILRLEKPALEFKPTGAESAYCVLPLNVVNDSGTLDIDFKFMEDIEKSEARI GIPSTKYSKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPL LDVDHTSSRLNLLTPRHLNQKGKALPLSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLLTA EELRAQTASDAGVGVRSLPVDFRYPNLDFGWKKSIDSKSFISSCNSSLAESDNYCKHSTTVVPEHAAHQGATRPSLENHD QMSVNCKRLPAESPAKLQSEVSTDLTAINGLSYNKNLANGSYDLVNRDFCQGNQLNYFKQEIPVQPTTSYPIQNLYNYEN QPKPSNECPLLSNTYLDGNANTSTSDGSPAVSTMPAMMNAVKALKDRMDSEQSPSVGYSSRTLGPNPGLILQALTLSNAS DGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDPPVNWLPPGYVV NQDKSNSEKWEKDEMTKDCLLANGKLGEACEEEEDLTWRAPKEEAEDEDDFLEYDQEHIQFIDSMLMGSGAFVRKISLSP FSASDSAYEWKMPKKASLGSMPFASGLEDFDYSSWDAMCYLDPSKAVEEDDFVVGFWNPSEENCGVDTGKQSISYDLHTE QCIADKSIADCVEALLGCYLTSCGERAAQLFLCSLGLKVLPVIKRTSREKALDPAQENGSSQQKSLSGSCASPVGPRSSA GKDLEYGCLKIPPRCMFDHPDAEKTLNHLISGFETFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILD YLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEMQGMDSELRRSE EDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLEVVWQVYYPMMQPLIEKFSANVPRSPVRELLEMEPETAKFSPAERT YDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLKANQPQVPNSGRGENLYFQGASDYKDHDGDYKDHDGSHHHH HHHH Q8R418 3.1.26.3 59-nt precursor of miR-15a Mus musculus 0.019017278999999998 1 UAGCAGCACAUAAUGGUUUGUGGAUGUUGAAAAGGUGCAGGCCAUACUGUGCUGCCUCA NR_029733.1 RISC-loading complex subunit TARBP2 isoform 1 Mus musculus 0.039991059 1 Spodoptera frugiperda LEVO MSEEDQGSGTTTGCGLPSIEQMLAANPGKTPISLLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDTSCTGQGPSK KAAKHKAAEVALKHLKGGSMLEPALEDSSSFSLLDSSPPEDTPVVAAEAAAPVPSAVLTRSPPMEMQPPVSPQQSECNPV GALQELVVQKGWRLPEYMVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKMLLRVHTVPLDARDGNEAEPD DDHFSIGVSSRLDGLRNRGPGCTWDSLRNSVGEKILSLRSCSVGSLGALGSACCSVLSELSEEQAFHVSYLDIEELSLSG LCQCLVELSTQPATVCYGSATTREAARGDAAHRALQYLRIMAGSKHHHHHHHH P97473 singleParticle particle 0.2 8.0 50.0 Tris 100.0 Sodium Chloride 1.0 Dithiotreitol 2.0 Calcium Chloride
The buffer was always prepared fresh in RNAse-free manner.
 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 K3 BIOQUANTUM (6k x 4k) COUNTING 48253 60.198 1 2219694 1 FOURIER SPACE 3.81 FSC 0.143 CUT-OFF cryoSPARC v3.3.1 afterwards processing in DeepEMhancer 437518 NOT APPLICABLE NOT APPLICABLE 2 430000.0 cryoSPARC v3.3.1 emd_14855.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 320.63998 320.63998 320.63998 90.0 90.0 90.0 X Y Z -0.012940883 1.7283056 0.00094697636 0.018903993 0.835 0.835 0.835 0.06 AUTHOR 7YYM A PDB experimental model 7YYM B PDB experimental model FLEXIBLE FIT
We used our previous deposition 7YYM as an initial model source. TARBP2 initial coordinates were predicted by AlphaFold. Initial local fitting was done using Chimera and then Coot's Real Space Refine Zone. PHENIX Real-space refinement was used for flexible fitting. ISOLDE was used for flexible fitting with torsion restraints defined for polypeptide chain and distance restraints for polyribonucleotides.
Ramachandran Plot, Rotamer Analysis, Density Fit Analysis, Correlation coefficient REAL 189.199999999999989 emd_14855_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 320.63998 320.63998 320.63998 90.0 90.0 90.0 X Y Z -0.24876049 0.6088656 0.000037878526 0.019382097 0.835 0.835 0.835 AUTHOR emd_14855_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 320.63998 320.63998 320.63998 90.0 90.0 90.0 X Y Z -0.21270722 0.60400796 0.000044222335 0.019389808 0.835 0.835 0.835 AUTHOR