9V42: DICER/26S-GU complex in dicing state

Cryo-EM structure of DICER/26S-GU complex in dicing state. Determined by electron microscopy at 3.37 Å resolution. Released 11 Mar 2026.

Method: Electron microscopy
Resolution: 3.37 Å
Organisms: synthetic construct, Homo sapiens
Chains: 2
Atoms: 6,879
Mol. weight: 239.57 kDa
Ligands: CA
Released: 11 Mar 2026

Explore 9V42 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9V42 contains 32 α-helices and 23 β-strands across 1 chain. 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 D: 32 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	769-770	2
β-strand	772	1	1
β-strand	802-805	4	2
α-helix	809-812	4
β-strand	816-817	2	3
β-strand	820	1	4
β-strand	823	1	4
β-strand	826-827	2	3
β-strand	833	1	1
α-helix	840-856	17
β-strand	873	1	5
β-strand	877-880	4	2
β-strand	881-883	3	6
β-strand	890-892	3	6
α-helix	894-902	9
α-helix	911-916	6
α-helix	918-920	3
β-strand	931-932	2	7
β-strand	945-946	2	7
α-helix	970-975	6
β-strand	988	1	8
β-strand	991	1	7
α-helix	995-997	3
β-strand	1005	1	9
β-strand	1013	1	9
α-helix	1018-1026	9
β-strand	1033	1	8
α-helix	1035-1038	4
α-helix	1045-1051	7
α-helix	1054-1073	20
α-helix	1294-1301	8
β-strand	1302	1	10
α-helix	1304-1306	3
α-helix	1314-1334	21
α-helix	1343-1352	10
α-helix	1356-1363	8
β-strand	1370	1	10
α-helix	1381-1382	2
β-strand	1385	1	5
α-helix	1548-1550	3
α-helix	1557-1573	17
α-helix	1576-1585	10
α-helix	1664-1673	10
α-helix	1680-1685	6
β-strand	1688	1	11
α-helix	1702-1722	21
α-helix	1729-1740	12
α-helix	1742-1751	10
β-strand	1759	1	11
α-helix	1767-1775	9
α-helix	1806-1822	17
α-helix	1827-1837	11
α-helix	1839-1846	8
α-helix	1853-1859	7
α-helix	1897-1911	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA (64-mer)	R	RNA	64	synthetic construct
Endoribonuclease Dicer	D	protein	1922	Homo sapiens	Q9UPY3 (AlphaFold model)

Sequence of entity 1 (R), FASTA

>9V42_1 RNA (64-MER) (chains R)
GGGAUAUUUCUCGCAGAUCUCAUGUGAAAAAAAAAACACAUGACAUCUGUGAGAAAUAUU
CUUA

Sequence of entity 2 (D), FASTA

>9V42_2 Endoribonuclease Dicer (chains D)
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

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Primary citation

DICER cleavage fidelity is governed by 5'-end binding pockets. Ngo, M.K., Le, C.T., Nguyen, T.A. Nature (2026) 653:611-620. DOI 10.1038/s41586-026-10211-5 · 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

Browse structure collections

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