2DNJ: Deoxyribonuclease I

DNase I-induced DNA conformation. 2 Å structure of a DNase I-octamer complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 31 Jan 1994.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Bos taurus
Chains: 3
Atoms: 2,553
Mol. weight: 33.55 kDa
Ligands: NAG
Released: 31 Jan 1994

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

Secondary structure: helices and β-sheets

2DNJ contains 12 α-helices and 18 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 A: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-11	10	1
α-helix	13-16	4
α-helix	19-30	12
β-strand	34-40	7	1
α-helix	46-55	10
β-strand	64-67	4	1
β-strand	71	1	2
β-strand	78	1	2
β-strand	79-84	6	1
β-strand	89-96	8	3
α-helix	112-113	2
β-strand	114-120	7	3
β-strand	127-132	6	3
α-helix	137-139	3
α-helix	140-158	19
β-strand	163-168	6	3
α-helix	178-183	6
α-helix	185-188	4
β-strand	192-194	3	3
β-strand	203	1	4
β-strand	212-217	6	3
α-helix	219-224	6
β-strand	225	1	5
α-helix	226	1
β-strand	231-232	2	1
α-helix	235-239	5
α-helix	243-249	7
β-strand	252	1	4
β-strand	255-258	4	1
β-strand	259	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(gpcpgpaptpcpgpc)-3'	B	DNA	8
5'-d(gpcpgpaptpc)-3'	C	DNA	6
Deoxyribonuclease I	A	protein	260	Bos taurus	P00639 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>2DNJ_1 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3' (chains B)
GCGATCGC

Sequence of entity 2 (C), FASTA

>2DNJ_2 5'-D(*GP*CP*GP*AP*TP*C)-3' (chains C)
GCGATC

Sequence of entity 3 (A), FASTA

>2DNJ_3 DEOXYRIBONUCLEASE I (chains A)
LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDP
NTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSS
HSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQ
WSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYG
LSNEMALAISDHYPVEVTLT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex. Lahm, A., Suck, D. J Mol Biol (1991) 222:645-667. DOI 10.1016/0022-2836(91)90502-W · PubMed

Other PDB entries of the same protein (UniProt P00639 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2A40 1.8 Å, Ternary complex of the WH2 domain of WAVE with Actin-DNAse I
3W3D 1.8 Å, Crystal structure of smooth muscle G actin DNase I complex
2A42 1.85 Å, Actin-DNAse I Complex
3DNI 2.0 Å, Crystallographic refinement and structure of DNase I at 2 Å resolution
2A3Z 2.08 Å, Ternary complex of the WH2 domain of WASP with Actin-DNAse I
1DNK 2.3 Å, The X-ray structure of the DNase I-D(GGTATACC)2 complex at 2.3 Å resolution
2D1K 2.5 Å, Ternary complex of the WH2 domain of mim with actin-dnase I
7NXV 2.55 Å, Crystal structure of the complex of DNase I/G-actin/PPP1R15A_582-621
2A41 2.6 Å, Ternary complex of the WH2 Domain of WIP with Actin-DNAse I
1ATN 2.8 Å, Atomic structure of the actin:DNASE I complex
9NB9 3.03 Å, Viral protein DP71L in complex with phosphorylated eIF2alpha (NTD) and protein…
9FJY 3.79 Å, Structure of the DNase I- and phalloidin-bound pointed end of F-actin (conformer 2).

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