4NGF: Endoribonuclease Dicer

Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 17-mer siRNA having 5'-p and UU-3' ends (3.1 Angstrom resolution). Determined by X-ray diffraction at 3.1 Å resolution. Released 5 Mar 2014.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 8
Atoms: 9,701
Mol. weight: 161.61 kDa
Released: 5 Mar 2014

Explore 4NGF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NGF contains 49 α-helices and 52 β-strands across 4 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: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	759-770	12	1
α-helix	780-782	3
α-helix	785-787	3
β-strand	791-796	6	1
β-strand	806-809	4	1
β-strand	813-824	12	1
α-helix	831-841	11
α-helix	842-847	6
β-strand	867-873	7	1
β-strand	880-882	3	1
α-helix	887-890	4
α-helix	909-910	2
β-strand	921-924	4	2
β-strand	935-941	7	2
β-strand	949	1	3
α-helix	950	1
β-strand	957	1	3
α-helix	958-966	9
β-strand	977-981	5	2
α-helix	1006-1020	15
β-strand	1022-1023	2	2
α-helix	1025-1027	3
β-strand	1028-1030	3	2
α-helix	1031	1
α-helix	1035-1041	7
α-helix	1044-1052	9

Chain B: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	759-770	12	4
α-helix	785-787	3
β-strand	791-796	6	4
β-strand	806-809	4	4
β-strand	813-824	12	4
α-helix	830-842	13
α-helix	843-847	5
β-strand	867-872	6	4
β-strand	881-882	2	4
α-helix	884-890	7
β-strand	921-924	4	5
β-strand	935-941	7	5
β-strand	949	1	6
α-helix	950	1
β-strand	957	1	6
α-helix	958-966	9
β-strand	977-981	5	5
α-helix	1007-1019	13
β-strand	1022-1023	2	5
α-helix	1025-1027	3
β-strand	1028-1030	3	5
α-helix	1031	1
α-helix	1035-1041	7
α-helix	1044-1052	9

Chain C: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	757-770	14	7
α-helix	780-782	3
α-helix	785-787	3
β-strand	791-796	6	7
β-strand	806-810	5	7
β-strand	813-827	15	7
α-helix	830-844	15
β-strand	867-873	7	7
β-strand	880-882	3	7
α-helix	884-890	7
α-helix	909-910	2
β-strand	921-924	4	8
β-strand	935-941	7	8
β-strand	949	1	9
α-helix	950	1
β-strand	957	1	9
α-helix	958-966	9
β-strand	977-981	5	8
α-helix	1009-1019	11
β-strand	1022-1023	2	8
α-helix	1025-1027	3
β-strand	1028-1030	3	8
α-helix	1031	1
α-helix	1035-1041	7
α-helix	1044-1052	9

Chain D: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	759-770	12	10
α-helix	780-782	3
α-helix	785-787	3
β-strand	791-796	6	10
α-helix	802-805	4
β-strand	806-810	5	10
β-strand	813-824	12	10
α-helix	830-842	13
α-helix	843-848	6
β-strand	867-872	6	10
β-strand	881-882	2	10
α-helix	884-890	7
β-strand	921-924	4	11
β-strand	935-941	7	11
β-strand	949	1	12
α-helix	950	1
β-strand	957	1	12
α-helix	958-964	7
β-strand	977-981	5	11
α-helix	1009-1020	12
β-strand	1022-1023	2	11
α-helix	1025-1027	3
β-strand	1028-1030	3	11
α-helix	1031	1
α-helix	1035-1041	7
α-helix	1044-1052	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endoribonuclease Dicer	A, B, C, D	protein	302	Homo sapiens	Q9UPY3 (AlphaFold model)
5'-r(pupcpgpapapgpgpupcpcpupupcpgpupup*u)-3'	E, F, G, H	RNA	17

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

>4NGF_1 Endoribonuclease Dicer (chains A, B, C, D)
SDQPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSG
EVTISIELKKSGFMLSLQMLELITRLHQYIFSHILRLEKPALEFKPTDADSAYCVLPLNV
VNDSSTLDIDFKFMEDIEKSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPH
RFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPR
HLNQKGKALPLSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHC
LL

Sequence of entity 2 (E, F, G, H), FASTA

>4NGF_2 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3' (chains E, F, G, H)
UCGAAGGUCCUUCGUUU

Primary citation

A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer. Tian, Y., Simanshu, D.K., Ma, J.B. et al. Mol Cell (2014) 53:606-616. DOI 10.1016/j.molcel.2014.01.003 · 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
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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