5DQT: Cas-DNA-22 complex

Crystal Structure of Cas-DNA-22 complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 11 Nov 2015.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Escherichia coli K12, Escherichia coli
Chains: 16
Atoms: 21,956
Mol. weight: 348.99 kDa
Released: 11 Nov 2015

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

Secondary structure: helices and β-sheets

5DQT contains 126 α-helices and 92 β-strands across 12 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	17-20	4	3
β-strand	24-28	5	4
β-strand	31-36	6	4
β-strand	39-44	6	4
α-helix	46-48	3
β-strand	51-54	4	3
β-strand	59-61	3	4
α-helix	62-70	9
α-helix	73	1
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	134-153	20
α-helix	175-198	24
α-helix	214-220	7
α-helix	228-238	11
α-helix	243-257	15
α-helix	260-273	14
α-helix	278-279	2

Chain B: 16 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	24-28	5	4
β-strand	31-35	5	4
β-strand	41-43	3	4
α-helix	46-48	3
β-strand	49-54	6	3
β-strand	59-61	3	4
α-helix	62-70	9
α-helix	73	1
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	134-155	22
α-helix	175-198	24
α-helix	214-223	10
α-helix	228-237	10
α-helix	243-257	15
α-helix	260-273	14
α-helix	278-279	2

Chain C: 15 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	24-28	5	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	59-61	3	2
α-helix	62-70	9
α-helix	73	1
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	134-155	22
α-helix	175-198	24
α-helix	214-223	10
α-helix	228-238	11
α-helix	243-257	15
α-helix	260-273	14

Chain D: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	1
β-strand	24-28	5	2
β-strand	31-36	6	2
β-strand	39-44	6	2
α-helix	46-48	3
β-strand	51-54	4	1
β-strand	59-61	3	2
α-helix	62-70	9
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	135-155	21
α-helix	175-198	24
α-helix	214-223	10
α-helix	228-238	11
α-helix	244-257	14
α-helix	260-273	14
α-helix	278-279	2

Chains E, M and N: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	6
α-helix	13-22	10
β-strand	24-27	4	6
β-strand	30-35	6	6
α-helix	37-50	14
β-strand	55-61	7	6
β-strand	68-73	6	6
β-strand	78-83	6	4
β-strand	86-91	6	4

Chain F: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	5
α-helix	13-22	10
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	79-83	5	2
β-strand	86-90	5	2

Chain I: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	9
β-strand	24-28	5	10
β-strand	31-36	6	10
β-strand	39-44	6	10
α-helix	46-48	3
β-strand	51-54	4	9
β-strand	59-61	3	10
α-helix	62-70	9
α-helix	73	1
β-strand	74-78	5	9
α-helix	80-82	3
β-strand	85-89	5	9
α-helix	96-107	12
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-156	23
α-helix	175-198	24
α-helix	214-223	10
α-helix	228-238	11
α-helix	243-257	15
α-helix	260-273	14
α-helix	278-280	3

Chain J: 16 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-13	3
β-strand	15-20	6	9
β-strand	23-28	6	10
β-strand	31-35	5	10
β-strand	41-43	3	10
α-helix	46-48	3
β-strand	49-54	6	9
β-strand	58-61	4	10
α-helix	62-70	9
α-helix	73	1
β-strand	74-78	5	9
α-helix	80-82	3
β-strand	84-89	6	9
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	229-237	9
α-helix	243-257	15
α-helix	260-273	14

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas1	A, B, C, D, I, J, K, L	protein	305	Escherichia coli K12	Q46896 (AlphaFold model)
CRISPR-associated endoribonuclease Cas2	E, F, M, N	protein	94	Escherichia coli K12	P45956 (AlphaFold model)
DNA (34-mer)	G, O	DNA	34	Escherichia coli
DNA (33-mer)	H, P	DNA	33	Escherichia coli

Sequence of entity 1 (A, B, C, D, I, J, K, L), FASTA

>5DQT_1 CRISPR-associated endonuclease Cas1 (chains A, B, C, D, I, J, K, L)
MTWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRV
SHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMF
ELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCI
SAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNP
GEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPAPPEDAQPVAIPLPVSLGDA
GHRSS

Sequence of entity 2 (E, F, M, N), FASTA

>5DQT_2 CRISPR-associated endoribonuclease Cas2 (chains E, F, M, N)
MSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAW
ATNTETGFEFQTFGLNRRTPVDLDGLRLVSFLPV

Sequence of entity 3 (G, O), FASTA

>5DQT_3 DNA (34-MER) (chains G, O)
TTTTTTCGTAGCTGAGTTGAGTCGATGCTTTTTT

Sequence of entity 4 (H, P), FASTA

>5DQT_4 DNA (33-MER) (chains H, P)
TTTTTTGCATCGACTCAACTCAGCTACGTTTTT

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
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
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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