5DLJ: Cas-DNA-N1 complex

Crystal Structure of Cas-DNA-N1 complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 11 Nov 2015.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Escherichia coli K12, Escherichia coli
Chains: 8
Atoms: 11,444
Mol. weight: 164.3 kDa
Released: 11 Nov 2015

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

Secondary structure: helices and β-sheets

5DLJ contains 65 α-helices and 46 β-strands across 6 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: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	4
β-strand	23-28	6	5
β-strand	31-36	6	5
β-strand	39-44	6	5
β-strand	51-54	4	4
β-strand	58-61	4	5
α-helix	62-71	10
α-helix	73	1
β-strand	74-78	5	4
α-helix	80-82	3
β-strand	85-89	5	4
α-helix	96-107	12
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-156	23
β-strand	166	1	6
β-strand	169	1	6
α-helix	170-172	3
α-helix	175-198	24
α-helix	214-223	10
α-helix	228-238	11
α-helix	243-258	16
α-helix	260-273	14
α-helix	278-280	3

Chain B: 17 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-13	3
β-strand	15-20	6	4
β-strand	23-28	6	5
β-strand	31-35	5	5
β-strand	41-43	3	5
α-helix	46-48	3
β-strand	49-54	6	4
β-strand	58-61	4	5
α-helix	62-71	10
α-helix	73	1
β-strand	74-78	5	4
α-helix	80-82	3
β-strand	84-89	6	4
α-helix	91-93	3
α-helix	96-107	12
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-156	23
α-helix	170-172	3
α-helix	175-197	23
α-helix	214-223	10
α-helix	228-237	10
α-helix	243-257	15
α-helix	260-273	14

Chain C: 17 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-13	3
β-strand	15-20	6	1
β-strand	23-28	6	2
β-strand	31-35	5	2
β-strand	41-43	3	2
α-helix	46-48	3
β-strand	49-54	6	1
β-strand	58-61	4	2
α-helix	62-71	10
α-helix	73	1
β-strand	74-78	5	1
α-helix	80-82	3
β-strand	84-89	6	1
α-helix	91-93	3
α-helix	96-107	12
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-156	23
α-helix	170-172	3
α-helix	175-197	23
α-helix	214-223	10
α-helix	228-237	10
α-helix	243-258	16
α-helix	260-273	14

Chain D: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	1
β-strand	23-28	6	2
β-strand	31-36	6	2
β-strand	39-44	6	2
β-strand	51-54	4	1
β-strand	58-61	4	2
α-helix	62-71	10
α-helix	73	1
β-strand	74-78	5	1
α-helix	80-82	3
β-strand	85-89	5	1
α-helix	96-107	12
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-156	23
β-strand	166	1	3
β-strand	169	1	3
α-helix	175-198	24
α-helix	214-223	10
α-helix	228-238	11
α-helix	243-258	16
α-helix	260-273	14
α-helix	278-280	3

Chains E and F: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	8
α-helix	13-20	8
β-strand	24-27	4	8
β-strand	30-35	6	8
α-helix	37-50	14
β-strand	55-61	7	8
β-strand	68-73	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas1	A, B, C, D	protein	280	Escherichia coli K12	Q46896 (AlphaFold model)
39-mer DNA N1-F	G	DNA	39	Escherichia coli
39-mer DNA N1-R	H	DNA	39	Escherichia coli
CRISPR-associated endoribonuclease Cas2	E, F	protein	78	Escherichia coli K12	P45956 (AlphaFold model)

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

>5DLJ_1 CRISPR-associated endonuclease Cas1 (chains A, B, C, D)
TWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRVS
HAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMFE
LRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCIS
AATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNPG
EPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPA

Sequence of entity 2 (G), FASTA

>5DLJ_2 39-mer DNA N1-F (chains G)
TTTTTTCGTAGCTGAGGGCCTCAGCTACGTTTTTTTTTT

Sequence of entity 3 (H), FASTA

>5DLJ_3 39-mer DNA N1-R (chains H)
TTTTTTCGTAGCTGAGGCCCTCAGCTACGTTTTTTTTTT

Sequence of entity 4 (E, F), FASTA

>5DLJ_4 CRISPR-associated endoribonuclease Cas2 (chains E, F)
MSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAW
ATNTETGFEFQTFGLNRR

Primary citation

Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems. Wang, J., Li, J., Zhao, H. et al. Cell (2015) 163:840-853. DOI 10.1016/j.cell.2015.10.008 · PubMed

Other PDB entries of the same protein (UniProt Q46896 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NKE 1.4 Å, High resolution structure of the C-terminal domain CRISP-associated protein Cas1 from…
3NKD 1.95 Å, Structure of CRISP-associated protein Cas1 from Escherichia coli str. K-12
4P6I 2.3 Å, Crystal structure of the Cas1-Cas2 complex from Escherichia coli
4QDL 2.7 Å, Crystal structure of E.coli Cas1-Cas2 complex
5DQZ 2.7 Å, Crystal Structure of Cas-DNA-PAM complex
5VVK 2.9 Å, Cas1-Cas2 bound to full-site mimic
5DS5 2.95 Å, Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA and Mg
5DQT 3.1 Å, Crystal Structure of Cas-DNA-22 complex
5DS4 3.2 Å, Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA
5VVL 3.31 Å, Cas1-Cas2 bound to full-site mimic with Ni
5DS6 3.35 Å, Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA with…
5WFE 3.64 Å, Cas1-Cas2-IHF-DNA holo-complex

Browse structure collections

About this viewer

MolViewer shows 5DLJ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.