5VVL: Cas1-Cas2

Cas1-Cas2 bound to full-site mimic with Ni. Determined by X-ray diffraction at 3.31 Å resolution. Released 2 Aug 2017.

Method: X-ray diffraction
Resolution: 3.31 Å
Organisms: Escherichia coli (strain K12), synthetic construct
Chains: 10
Atoms: 11,762
Mol. weight: 201.22 kDa
Ligands: NI
Released: 2 Aug 2017

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

Secondary structure: helices and β-sheets

5VVL contains 56 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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	1
β-strand	23-28	6	2
β-strand	31-35	5	2
β-strand	42-44	3	2
β-strand	51-54	4	1
β-strand	58-61	4	2
α-helix	62-71	10
β-strand	74-78	5	1
α-helix	80-82	3
β-strand	85-89	5	1
α-helix	96-107	12
α-helix	109-123	15
α-helix	127-129	3
α-helix	134-156	23
α-helix	175-198	24
α-helix	214-222	9
α-helix	224-237	14
α-helix	243-257	15
α-helix	260-273	14

Chain B: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
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
β-strand	74-78	5	1
α-helix	80-82	3
β-strand	84-89	6	1
α-helix	96-107	12
α-helix	109-123	15
α-helix	127-129	3
α-helix	134-156	23
α-helix	167-169	3
α-helix	176-198	23
α-helix	214-222	9
α-helix	224-238	15
α-helix	243-257	15
α-helix	260-273	14

Chain C: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	18-20	3	3
β-strand	23-28	6	4
β-strand	31-36	6	4
β-strand	42-44	3	4
β-strand	51-54	4	3
β-strand	58-60	3	4
α-helix	62-71	10
β-strand	74-78	5	3
α-helix	80-82	3
β-strand	85-89	5	3
α-helix	96-107	12
α-helix	109-123	15
α-helix	127-129	3
α-helix	134-156	23
α-helix	170-172	3
α-helix	175-198	24
α-helix	214-220	7
α-helix	224-226	3
α-helix	228-238	11
α-helix	243-258	16
α-helix	260-273	14

Chain D: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	15-20	6	3
β-strand	23-28	6	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	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	214-222	9
α-helix	224-228	5
α-helix	229-238	10
α-helix	243-258	16
α-helix	260-272	13

Chains E and 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	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	308	Escherichia coli (strain K12)	Q46896 (AlphaFold model)
CRISPR-associated endoribonuclease Cas2	E, F	protein	103	Escherichia coli (strain K12)	P45956 (AlphaFold model)
DNA (11-mer)	G	DNA	11	synthetic construct
DNA (11-mer)	H	DNA	11	synthetic construct
DNA (58-mer)	J	DNA	58	synthetic construct
DNA (58-mer)	K	DNA	58	synthetic construct

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

>5VVL_1 CRISPR-associated endonuclease Cas1 (chains A, B, C, D)
SFTMTWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPG
TRVSHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVR
KMFELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTIN
QCISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIAR
RNPGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPAPPEDAQPVAIPLPVSL
GDAGHRSS

Sequence of entity 2 (E, F), FASTA

>5VVL_2 CRISPR-associated endoribonuclease Cas2 (chains E, F)
MSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAW
ATNTETGFEFQTFGLNRRTPVDLDGLRLVSFLPVGSSENLYFQ

Sequence of entity 3 (G), FASTA

>5VVL_3 DNA (11-MER) (chains G)
GCCCCAGTAGC

Sequence of entity 4 (H), FASTA

>5VVL_4 DNA (11-MER) (chains H)
GACCACCAGTG

Sequence of entity 5 (J), FASTA

>5VVL_5 DNA (58-MER) (chains J)
CACTGGTGGTCGCCGCGGTTTATCCCCGCTGGCGCGGGGAACACTCTAAGATATTAGA

Sequence of entity 6 (K), FASTA

>5VVL_6 DNA (58-MER) (chains K)
GCTACTGGGGCCGAGGGTGTTCCCCGCGCCAGCGGGGATAAACCGAGCAGATATGCTC

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	22

Primary citation

Structures of the CRISPR genome integration complex. Wright, A.V., Liu, J.J., Knott, G.J. et al. Science (2017) 357:1113-1118. DOI 10.1126/science.aao0679 · 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
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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