2EB1: C-Terminal RNase III Domain of Human Dicer

Crystal Structure of the C-Terminal RNase III Domain of Human Dicer. Determined by X-ray diffraction at 2.0 Å resolution. Released 6 Nov 2007.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,404
Mol. weight: 71.06 kDa
Ligands: MG
Released: 6 Nov 2007

Explore 2EB1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2EB1 contains 30 α-helices and 6 β-strands across 3 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: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	22-29	8
β-strand	30	1	1
α-helix	44-64	21
α-helix	71-81	11
α-helix	84-93	10
α-helix	96-98	3
β-strand	101	1	1
α-helix	105-120	16
α-helix	145-146	2
α-helix	148-164	17
α-helix	169-189	21

Chain B: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	22-29	8
β-strand	30	1	2
α-helix	44-64	21
α-helix	71-81	11
α-helix	84-93	10
α-helix	96-98	3
β-strand	101	1	2
α-helix	105-120	16
α-helix	148-164	17
α-helix	169-189	21

Chain C: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	8-15	8
α-helix	22-28	7
β-strand	30	1	3
α-helix	44-64	21
α-helix	71-81	11
α-helix	84-93	10
α-helix	96-98	3
β-strand	101	1	3
α-helix	105-119	15
α-helix	145-146	2
α-helix	148-164	17
α-helix	169-189	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endoribonuclease Dicer	A, B, C	protein	200	Homo sapiens	Q9UPY3 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>2EB1_1 Endoribonuclease Dicer (chains A, B, C)
MNHLISGFENFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITK
HLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLE
KNEMQGMDSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMM
RPLIEKFSANVPRSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	6

Primary citation

Homodimeric Structure and Double-stranded RNA Cleavage Activity of the C-terminal RNase III Domain of Human Dicer. Takeshita, D., Zenno, S., Lee, W.C. et al. J Mol Biol (2007) 374:106-120. DOI 10.1016/j.jmb.2007.08.069 · 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…
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
21CN 3.21 Å, Cryo-EM structure of DICER with pre-mir-517a-GU in dicing state

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