5ZAK: Endoribonuclease Dicer

Cryo-EM structure of human Dicer and its complexes with a pre-miRNA substrate. Determined by electron microscopy at 4.4 Å resolution. Released 9 May 2018.

Method
Electron microscopy
Resolution
4.4 Å
Organism
Homo sapiens
Chains
2
Atoms
11,112
Mol. weight
258.03 kDa
Released
9 May 2018

Explore 5ZAK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ZAK contains 60 α-helices and 45 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 57 helices, 41 β-strands

ElementResiduesLengthSheet
α-helix46-538
β-strand61-6331
α-helix70-8415
β-strand97-9932
α-helix103-11412
β-strand149-15022
α-helix152-1587
β-strand16813
β-strand172-17322
α-helix177-1793
α-helix186-1938
β-strand19813
β-strand202-20322
β-strand204-20631
α-helix219-23012
β-strand23511
β-strand250-25124
α-helix265-28420
α-helix296-2972
α-helix298-3025
α-helix303-31311
α-helix315-33521
α-helix339-35820
α-helix378-3858
β-strand44615
α-helix452-4609
β-strand46916
β-strand474-47527
β-strand482-48327
α-helix498-50912
α-helix511-5155
β-strand51716
β-strand534-53525
α-helix543-5508
β-strand558-55924
β-strand560-56125
α-helix571-58919
α-helix631-6388
β-strand65618
β-strand66418
α-helix687-70317
α-helix714-72512
β-strand768-77369
β-strand776-780510
α-helix781-7822
α-helix795-7973
β-strand800-80679
α-helix813-8153
β-strand817-819310
β-strand823-826410
β-strand829-83689
α-helix840-85415
β-strand864111
β-strand868111
β-strand877-88489
β-strand889-89249
α-helix895-9028
α-helix904-9063
α-helix924-9263
β-strand930-934512
β-strand945-947312
α-helix958-9603
α-helix968-9747
α-helix988-9892
β-strand990-992312
α-helix1003-10097
α-helix1016-10172
α-helix1018-10236
α-helix1024-10307
β-strand1038-1041412
α-helix1045-10517
α-helix1054-107118
α-helix1295-13017
α-helix1313-133220
α-helix1340-135112
α-helix1353-13619
α-helix1365-13673
α-helix1559-157315
α-helix1576-15838
α-helix1584-15885
α-helix1595-15984
α-helix1657-167317
α-helix1680-16867
β-strand1688113
α-helix1702-172120
α-helix1729-173810
α-helix1742-175110
β-strand1759113
α-helix1763-177311
α-helix1806-182217
α-helix1827-184418
α-helix1854-18574
β-strand1865114
β-strand1872115
β-strand1878115
β-strand1882-1884314
β-strand1888-1890314
α-helix1897-191014
Chain B: 3 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix294-30411
β-strand310116
β-strand313116
α-helix317-3182
β-strand324-328516
β-strand336-340516
α-helix344-36118

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Endoribonuclease DicerAprotein1922Homo sapiensQ9UPY3 (AlphaFold model)
RISC-loading complex subunit TARBP2Bprotein366Homo sapiensQ15633 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>5ZAK_1 Endoribonuclease Dicer (chains A)
MKSPALQPLSMAGLQLMTPASSPMGPFFGLPWQQEAIHDNIYTPRKYQVELLEAALDHNT
IVCLNTGSGKTFIAVLLTKELSYQIRGDFSRNGKRTVFLVNSANQVAQQVSAVRTHSDLK
VGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLA
ILDHPYREIMKLCENCPSCPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATDL
VVLDRYTSQPCEIVVDCGPFTDRSGLYERLLMELEEALNFINDCNISVHSKERDSTLISK
QILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELHRKFLLFTDTFLRKIHALCE
EHFSPASLDLKFVTPKVIKLLEILRKYKPYERQQFESVEWYNNRNQDNYVSWSDSEDDDE
DEEIEEKEKPETNFPSPFTNILCGIIFVERRYTAVVLNRLIKEAGKQDPELAYISSNFIT
GHGIGKNQPRNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLP
TEYRSYVQSKGRARAPISNYIMLADTDKIKSFEEDLKTYKAIEKILRNKCSKSVDTGETD
IDPVMDDDDVFPPYVLRPDDGGPRVTINTAIGHINRYCARLPSDPFTHLAPKCRTRELPD
GTFYSTLYLPINSPLRASIVGPPMSCVRLAERVVALICCEKLHKIGELDDHLMPVGKETV
KYEEELDLHDEEETSVPGRPGSTKRRQCYPKAIPECLRDSYPRPDQPCYLYVIGMVLTTP
LPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTISIELKKSGFMLSL
QMLELITRLHQYIFSHILRLEKPALEFKPTDADSAYCVLPLNVVNDSSTLDIDFKFMEDI
EKSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKF
PSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQKGKALPLSSAEKR
KAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLLTAEELRAQTASDAGV
GVRSLPADFRYPNLDFGWKKSIDSKSFISISNSSSAENDNYCKHSTIVPENAAHQGANRT
SSLENHDQMSVNCRTLLSESPGKLHVEVSADLTAINGLSYNQNLANGSYDLANRDFCQGN
QLNYYKQEIPVQPTTSYSIQNLYSYENQPQPSDECTLLSNKYLDGNANKSTSDGSPVMAV
MPGTTDTIQVLKGRMDSEQSPSIGYSSRTLGPNPGLILQALTLSNASDGFNLERLEMLGD
SFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDPPVNW
LPPGYVVNQDKSNTDKWEKDEMTKDCMLANGKLDEDYEEEDEEEESLMWRAPKEEADYED
DFLEYDQEHIRFIDNMLMGSGAFVKKISLSPFSTTDSAYEWKMPKKSSLGSMPFSSDFED
FDYSSWDAMCYLDPSKAVEEDDFVVGFWNPSEENCGVDTGKQSISYDLHTEQCIADKSIA
DCVEALLGCYLTSCGERAAQLFLCSLGLKVLPVIKRTDREKALCPTRENFNSQQKNLSVS
CAAASVASSRSSVLKDSEYGCLKIPPRCMFDHPDADKTLNHLISGFENFEKKINYRFKNK
AYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALV
NNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEKNEMQGMDSELRRSEEDEEKEE
DIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPLIEKFSANVPRSPVRELLEM
EPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLKANQPQVP
NS
Sequence of entity 2 (B), FASTA
>5ZAK_2 RISC-loading complex subunit TARBP2 (chains B)
MSEEEQGSGTTTGCGLPSIEQMLAANPGKTPISLLQEYGTRIGKTPVYDLLKAEGQAHQP
NFTFRVTVGDTSCTGQGPSKKAAKHKAAEVALKHLKGGSMLEPALEDSSSFSPLDSSLPE
DIPVFTAAAAATPVPSVVLTRSPPMELQPPVSPQQSECNPVGALQELVVQKGWRLPEYTV
TQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKMLLRVHTVPLDARDGNEVEP
DDDHFSIGVGSRLDGLRNRGPGCTWDSLRNSVGEKILSLRSCSLGSLGALGPACCRVLSE
LSEEQAFHVSYLDIEELSLSGLCQCLVELSTQPATVCHGSATTREAARGEAARRALQYLK
IMAGSK

Primary citation

Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate. Liu, Z., Wang, J., Cheng, H. et al. Cell (2018) 173:1191-1203.e12. DOI 10.1016/j.cell.2018.03.080 · PubMed

Other PDB entries of the same protein (UniProt Q9UPY3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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