5ZAM: Endoribonuclease Dicer

Cryo-EM structure of human Dicer and its complexes with a pre-miRNA substrate. Determined by electron microscopy at 5.7 Å resolution. Released 9 May 2018.

Method: Electron microscopy
Resolution: 5.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 12,045
Mol. weight: 281.41 kDa
Released: 9 May 2018

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

Secondary structure: helices and β-sheets

5ZAM contains 54 α-helices and 37 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: 51 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	46-53	8
α-helix	54-56	3
β-strand	62	1	1
β-strand	63	1	2
α-helix	70-85	16
β-strand	97-99	3	3
α-helix	103-113	11
β-strand	121	1	4
β-strand	147	1	4
β-strand	148-150	3	3
α-helix	152-158	7
β-strand	171-173	3	3
α-helix	177-179	3
α-helix	186-193	8
β-strand	201-203	3	3
β-strand	206	1	2
α-helix	219-230	12
β-strand	235	1	1
α-helix	239-243	5
β-strand	253-255	3	5
β-strand	260	1	6
α-helix	265-282	18
α-helix	296-335	40
α-helix	339-362	24
β-strand	371	1	7
α-helix	378-383	6
β-strand	388	1	6
β-strand	446-447	2	5
α-helix	451-460	10
β-strand	465	1	7
α-helix	498-508	11
α-helix	511-515	5
β-strand	534-537	4	5
α-helix	544-550	7
β-strand	560-563	4	5
α-helix	570-593	24
α-helix	630-636	7
α-helix	688-705	18
α-helix	715-723	9
β-strand	768	1	8
β-strand	769-773	5	9
β-strand	774-777	4	10
α-helix	795-797	3
β-strand	801-806	6	9
α-helix	814-815	2
β-strand	816-819	4	10
β-strand	824-828	5	10
β-strand	831	1	9
β-strand	836	1	8
α-helix	840-858	19
β-strand	879-881	3	9
β-strand	882-884	3	11
β-strand	889-891	3	11
α-helix	894-902	9
α-helix	904-906	3
β-strand	931-934	4	12
β-strand	945-951	7	12
α-helix	968-974	7
β-strand	987-992	6	12
α-helix	1003-1011	9
α-helix	1016-1027	12
β-strand	1032-1033	2	12
β-strand	1038-1041	4	12
α-helix	1045-1051	7
α-helix	1054-1071	18
α-helix	1295-1299	5
α-helix	1314-1332	19
α-helix	1340-1350	11
α-helix	1353-1361	9
α-helix	1365-1368	4
α-helix	1559-1572	14
α-helix	1576-1586	11
α-helix	1614-1617	4
α-helix	1655-1657	3
α-helix	1659-1673	15
α-helix	1681-1687	7
α-helix	1693-1697	5
α-helix	1702-1721	20
α-helix	1729-1738	10
α-helix	1742-1751	10
α-helix	1763-1775	13
α-helix	1808-1822	15
α-helix	1827-1847	21
α-helix	1853-1860	8
α-helix	1897-1910	14

Chain B: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	293-304	12
β-strand	309-312	4	13
α-helix	317-318	2
β-strand	325-329	5	13
β-strand	335-339	5	13
α-helix	344-362	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endoribonuclease Dicer	A	protein	1922	Homo sapiens	Q9UPY3 (AlphaFold model)
RISC-loading complex subunit TARBP2	B	protein	366	Homo sapiens	Q15633 (AlphaFold model)
RNA (73-mer)	C	RNA	73	Homo sapiens

Sequence of entity 1 (A), FASTA

>5ZAM_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

>5ZAM_2 RISC-loading complex subunit TARBP2 (chains B)
MSEEEQGSGTTTGCGLPSIEQMLAANPGKTPISLLQEYGTRIGKTPVYDLLKAEGQAHQP
NFTFRVTVGDTSCTGQGPSKKAAKHKAAEVALKHLKGGSMLEPALEDSSSFSPLDSSLPE
DIPVFTAAAAATPVPSVVLTRSPPMELQPPVSPQQSECNPVGALQELVVQKGWRLPEYTV
TQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKMLLRVHTVPLDARDGNEVEP
DDDHFSIGVGSRLDGLRNRGPGCTWDSLRNSVGEKILSLRSCSLGSLGALGPACCRVLSE
LSEEQAFHVSYLDIEELSLSGLCQCLVELSTQPATVCHGSATTREAARGEAARRALQYLK
IMAGSK

Sequence of entity 3 (C), FASTA

>5ZAM_3 RNA (73-mer) (chains C)
UGAGGUAGUAGGUUGUAUAGUUUUAGGGUCACACCCACCACUGGGAGAUAACUAUACAAU
CUACUGUCUUACC

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:

4NGD 1.96 Å, Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-mer…
2EB1 2.0 Å, Crystal Structure of the C-Terminal RNase III Domain of Human Dicer
4NGC 2.1 Å, Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-mer…
4NGB 2.25 Å, Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-mer…
4NH5 2.55 Å, Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 14-mer…
4NH6 2.55 Å, Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 15-mer…
4NGG 2.6 Å, Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 13-mer…
4NH3 2.62 Å, Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 13-mer…
21CB 3.0 Å, Cryo-EM structure of DICER with pre-mir-517a-GU in pre-dicing state
7XW2 3.04 Å, Cryo-EM structure of human DICER-pre-miRNA in a dicing state
4NGF 3.1 Å, Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 17-mer…
4WYQ 3.2 Å, Crystal structure of the Dicer-TRBP interface

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