5DQZ: Cas-DNA-PAM complex

Crystal Structure of Cas-DNA-PAM complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 11 Nov 2015.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Escherichia coli K12, Escherichia coli
Chains: 8
Atoms: 11,765
Mol. weight: 176.05 kDa
Ligands: MG
Released: 11 Nov 2015

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

Secondary structure: helices and β-sheets

5DQZ contains 64 α-helices and 54 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, 11 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	5
β-strand	23-28	6	6
β-strand	31-36	6	6
β-strand	39-44	6	6
α-helix	46-48	3
β-strand	51-54	4	5
β-strand	58-61	4	6
α-helix	62-71	10
α-helix	73	1
β-strand	74-78	5	5
α-helix	80-82	3
β-strand	85-89	5	5
α-helix	96-107	12
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-155	22
β-strand	166	1	7
β-strand	169	1	7
α-helix	175-198	24
β-strand	208	1	8
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 B: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	15-20	6	5
β-strand	23-28	6	6
β-strand	31-35	5	6
β-strand	41-43	3	6
α-helix	46-48	3
β-strand	49-54	6	5
β-strand	58-61	4	6
α-helix	62-70	9
α-helix	73	1
β-strand	74-78	5	5
α-helix	80-82	3
β-strand	84-89	6	5
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
α-helix	278-283	6
β-strand	287	1	8
α-helix	288	1
α-helix	292-295	4

Chain C: 16 helices, 9 β-strands

Element	Residues	Length	Sheet
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	62-70	9
α-helix	73	1
β-strand	74-78	5	1
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
α-helix	278-283	6
β-strand	287	1	4
α-helix	288	1
α-helix	292-295	4

Chain D: 13 helices, 11 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
α-helix	46-48	3
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	134-155	22
β-strand	166	1	3
β-strand	169	1	3
α-helix	175-198	24
β-strand	208	1	4
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

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

Element	Residues	Length	Sheet
β-strand	2-9	8	10
α-helix	13-20	8
β-strand	24-27	4	10
β-strand	30-35	6	10
α-helix	37-50	14
β-strand	55-61	7	10
β-strand	68-73	6	10
β-strand	78-83	6	2
β-strand	86-91	6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas1	A, B, C, D	protein	305	Escherichia coli K12	Q46896 (AlphaFold model)
DNA (36-mer)	G	DNA	36	Escherichia coli
DNA (36-mer)	H	DNA	36	Escherichia coli
CRISPR-associated endoribonuclease Cas2	E, F	protein	94	Escherichia coli K12	P45956 (AlphaFold model)

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

>5DQZ_1 CRISPR-associated endonuclease Cas1 (chains A, B, C, D)
MTWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRV
SHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMF
ELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCI
SAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNP
GEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPAPPEDAQPVAIPLPVSLGDA
GHRSS

Sequence of entity 2 (G), FASTA

>5DQZ_2 DNA (36-MER) (chains G)
TTTTTCGTAGCTGAGGGCCTCAGCTACGTTTTCTTT

Sequence of entity 3 (H), FASTA

>5DQZ_3 DNA (36-MER) (chains H)
TTTTTCGTAGCTGAGGCCCTCAGCTACGTTTTCTTT

Sequence of entity 4 (E, F), FASTA

>5DQZ_4 CRISPR-associated endoribonuclease Cas2 (chains E, F)
MSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAW
ATNTETGFEFQTFGLNRRTPVDLDGLRLVSFLPV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

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
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 more

5DQZ is part of these collections:

CRISPR and genome editing

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