5DS5: CRISPR-associated endonuclease Cas1

Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA and Mg. Determined by X-ray diffraction at 2.95 Å resolution. Released 28 Oct 2015.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Escherichia coli (strain K12), Enterobacteria phage M13
Chains: 8
Atoms: 10,719
Mol. weight: 174 kDa
Ligands: MG
Released: 28 Oct 2015

Explore 5DS5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DS5 contains 60 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: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	1
β-strand	23-26	4	2
β-strand	32-35	4	2
β-strand	43-44	2	2
β-strand	51-54	4	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	134-155	22
α-helix	175-198	24
α-helix	214-223	10
α-helix	224-228	5
α-helix	229-238	10
α-helix	243-257	15
α-helix	260-273	14

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	1
β-strand	23-28	6	2
β-strand	31-35	5	2
β-strand	41-44	4	2
α-helix	46-48	3
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	167-169	3
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	260-273	14
α-helix	278-279	2

Chain C: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	3
β-strand	23-26	4	4
β-strand	32-35	4	4
β-strand	41-44	4	4
β-strand	51-54	4	3
β-strand	58-61	4	4
α-helix	62-70	9
β-strand	74-78	5	3
α-helix	80-82	3
β-strand	85-89	5	3
α-helix	96-107	12
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-155	22
α-helix	175-198	24
α-helix	214-223	10
α-helix	224-228	5
α-helix	229-238	10
α-helix	243-257	15
α-helix	260-273	14

Chain D: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-13	3
β-strand	15-20	6	3
β-strand	23-26	4	4
α-helix	28-30	3
β-strand	32-35	4	4
β-strand	41-44	4	4
β-strand	49-54	6	3
β-strand	58-61	4	4
α-helix	62-70	9
β-strand	74-78	5	3
α-helix	80-82	3
β-strand	84-89	6	3
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	260-273	14

Chains E and F: 2 helices, 7 β-strands

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

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 (28-mer)	G	DNA	28	Enterobacteria phage M13
DNA (28-mer)	H	DNA	28	Enterobacteria phage M13

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

>5DS5_1 CRISPR-associated endonuclease Cas1 (chains A, B, C, D)
SMTWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTR
VSHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKM
FELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQC
ISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRN
PGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPAPPEDAQPVAIPLPVSLGD
AGHRSS

Sequence of entity 2 (E, F), FASTA

>5DS5_2 CRISPR-associated endoribonuclease Cas2 (chains E, F)
MMSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMA
WATNTETGFEFQTFGLNRRTPVDLDGLRLVSFLPVGSSENLYFQ

Sequence of entity 3 (G), FASTA

>5DS5_3 DNA (28-MER) (chains G)
AAACACCAGAACGAGTAGTAAATTGGGC

Sequence of entity 4 (H), FASTA

>5DS5_4 DNA (28-MER) (chains H)
ATTTACTACTCGTTCTGGTGTTTCTCGT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	5

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
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

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