2024-07-24 REL PDBe PDBe PDBe 2022-04-27 2022-11-16 2022-11-16 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 "dicing state" with pre-miR-15a substrate Zanova M Zapletal D Kubicek K Stefl R Pinkas M Novacek J endoribonuclease, dsRNA, complex, gene silencing, post-transcriptional, catalytic complex, 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-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
 7zpi FULLOVERLAP Dicing state of mouse somatic dicer with pre-mir-15a Dicing state of mouse somatic dicer with pre-mir-15a 0 1 2
TARBP2 present in the sample but its density was not observed in final 3D EM map
 Dicing state of mouse somatic dicer 1 1 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 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 27 FOURIER SPACE 5.91 FSC 0.143 CUT-OFF cryoSPARC v3.3.1 64038 NOT APPLICABLE NOT APPLICABLE 50 2600.0 cryoSPARC v3.3.1 emd_14854.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 -0.18801418 0.4673915 -0.00011640316 0.0143638095 0.835 0.835 0.835 0.124 AUTHOR 7YYN A PDB experimental model 7YYN B PDB experimental model FLEXIBLE FIT
We used our previous deposition 7YYN as an initial model source. Initial local fitting was done using Chimera. 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 520.0 emd_14854_additional_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 -0.004433688 1.4487289 0.00033463904 0.010730902 0.835 0.835 0.835 AUTHOR Sharpened version of main EM map emd_14854_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 -0.86537504 0.8504824 0.00022137562 0.06099593 0.835 0.835 0.835 AUTHOR emd_14854_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 -0.83948815 0.8547145 0.00020175385 0.061287764 0.835 0.835 0.835 AUTHOR