5DS6: CRISPR-associated endonuclease Cas1

Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA with splayed ends. Determined by X-ray diffraction at 3.35 Å resolution. Released 28 Oct 2015.

Method: X-ray diffraction
Resolution: 3.35 Å
Organisms: Escherichia coli (strain K12), Enterobacteria phage M13
Chains: 8
Atoms: 10,540
Mol. weight: 176.91 kDa
Released: 28 Oct 2015

Explore 5DS6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DS6 contains 61 α-helices and 49 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	16-20	5	1
β-strand	23-27	5	2
β-strand	32-35	4	2
β-strand	43-44	2	2
β-strand	49-54	6	1
β-strand	58-61	4	2
α-helix	62-70	9
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
α-helix	176-198	23
α-helix	214-223	10
α-helix	224-228	5
α-helix	229-237	9
α-helix	243-257	15
α-helix	260-272	13
α-helix	273-275	3
α-helix	278-280	3

Chain B: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	15-20	6	1
β-strand	23-27	5	2
β-strand	32-35	4	2
β-strand	41-42	2	3
β-strand	43	1	2
β-strand	49-54	6	1
β-strand	58-61	4	2
α-helix	62-70	9
β-strand	74-78	5	1
α-helix	80-82	3
β-strand	84-89	6	1
α-helix	96-107	12
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-156	23
α-helix	176-198	23
α-helix	214-223	10
α-helix	224-228	5
α-helix	229-238	10
α-helix	243-257	15
α-helix	260-272	13
α-helix	273-275	3

Chain C: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	4
β-strand	23-28	6	5
β-strand	31-35	5	5
β-strand	42-44	3	5
β-strand	51-54	4	4
β-strand	58-61	4	5
α-helix	62-71	10
β-strand	74-78	5	4
α-helix	80-82	3
β-strand	85-89	5	4
α-helix	96-107	12
α-helix	114-124	11
α-helix	127-129	3
α-helix	134-155	22
α-helix	176-198	23
α-helix	214-223	10
α-helix	224-228	5
α-helix	229-238	10
α-helix	243-257	15
α-helix	260-272	13
α-helix	273-275	3

Chain D: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	15	1	6
β-strand	18-20	3	4
β-strand	23-27	5	5
β-strand	32-35	4	5
β-strand	41-43	3	5
α-helix	46-48	3
β-strand	49	1	6
β-strand	51-54	4	4
β-strand	58-61	4	5
α-helix	62-70	9
β-strand	74-78	5	4
α-helix	80-82	3
β-strand	84-89	6	4
α-helix	96-107	12
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-156	23
α-helix	177-198	22
α-helix	214-227	14
α-helix	228-232	5
α-helix	233-238	6
α-helix	243-257	15
α-helix	260-271	12

Chains E and F: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	7
α-helix	13-18	6
α-helix	19-21	3
β-strand	24-27	4	7
β-strand	30-35	6	7
α-helix	37-50	14
β-strand	55-61	7	7
β-strand	68-73	6	7
β-strand	78-83	6	5
β-strand	86-91	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas1	A, B, C, D	protein	306	Escherichia coli (strain K12)	Q46896 (AlphaFold model)
CRISPR-associated endoribonuclease Cas2	E, F	protein	104	Escherichia coli (strain K12)	P45956 (AlphaFold model)
DNA (29-mer)	G	DNA	33	Enterobacteria phage M13
DNA (28-mer)	H	DNA	33	Enterobacteria phage M13

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

>5DS6_1 CRISPR-associated endonuclease Cas1 (chains A, B, C, D)
SMTWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTR
VSHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKM
FELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQC
ISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRN
PGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPAPPEDAQPVAIPLPVSLGD
AGHRSS

Sequence of entity 2 (E, F), FASTA

>5DS6_2 CRISPR-associated endoribonuclease Cas2 (chains E, F)
MMSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMA
WATNTETGFEFQTFGLNRRTPVDLDGLRLVSFLPVGSSENLYFQ

Sequence of entity 3 (G), FASTA

>5DS6_3 DNA (29-MER) (chains G)
CATCTAAACACCAGAACGAGTAGTAAATTGGGC

Sequence of entity 4 (H), FASTA

>5DS6_4 DNA (28-MER) (chains H)
TAAACATTTACTACTCGTTCTGGTGTTTCTCGT

Primary citation

Foreign DNA capture during CRISPR-Cas adaptive immunity. Nunez, J.K., Harrington, L.B., Kranzusch, P.J. et al. Nature (2015) 527:535-538. DOI 10.1038/nature15760 · 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
5DLJ 2.6 Å, Crystal Structure of Cas-DNA-N1 complex
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
5WFE 3.64 Å, Cas1-Cas2-IHF-DNA holo-complex

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