5WFE: Cas1-Cas2-IHF-DNA holo-complex

Cas1-Cas2-IHF-DNA holo-complex. Determined by electron microscopy at 3.64 Å resolution. Released 2 Aug 2017.

Method: Electron microscopy
Resolution: 3.64 Å
Organisms: Escherichia coli K-12, synthetic construct, Escherichia coli S88
Chains: 12
Atoms: 15,523
Mol. weight: 253.91 kDa
Released: 2 Aug 2017

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

Secondary structure: helices and β-sheets

5WFE contains 63 α-helices and 59 β-strands across 8 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	1
β-strand	24-27	4	2
β-strand	32-35	4	2
β-strand	41	1	2
β-strand	44	1	2
β-strand	51-54	4	1
β-strand	59-61	3	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	109-123	15
α-helix	127-129	3
α-helix	134-156	23
α-helix	176-198	23
α-helix	214-222	9
α-helix	228-238	11
α-helix	243-258	16
α-helix	260-273	14

Chain B: 16 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	214-223	10
α-helix	224-228	5
α-helix	229-238	10
α-helix	243-258	16
α-helix	260-273	14
α-helix	278-279	2

Chain C: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	3
β-strand	24-27	4	4
β-strand	32-35	4	4
β-strand	41	1	4
β-strand	44	1	4
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	109-123	15
α-helix	127-129	3
α-helix	134-155	22
α-helix	176-198	23
α-helix	214-222	9
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	11-13	3
β-strand	15-20	6	3
β-strand	23-27	5	4
β-strand	32-35	4	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
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	134-156	23
α-helix	167-169	3
α-helix	176-198	23
α-helix	214-238	25
α-helix	243-258	16
α-helix	260-273	14

Chain E: 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	2
β-strand	86-91	6	2

Chain F: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	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	68-74	7	6
β-strand	78-83	6	4
β-strand	86-91	6	4

Chain K: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	7
α-helix	5-16	12
α-helix	20-39	20
β-strand	44-46	3	8
β-strand	50-57	8	8
β-strand	60	1	9
β-strand	73	1	9
β-strand	76-83	8	8
α-helix	85-92	8

Chain L: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
α-helix	19-38	20
β-strand	43-45	3	7
β-strand	49-56	8	7
β-strand	60-62	3	10
β-strand	69-71	3	10
β-strand	75-82	8	7
α-helix	84-90	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas1	A, B, C, D	protein	305	Escherichia coli K-12	Q46896 (AlphaFold model)
CRISPR-associated endoribonuclease Cas2	E, F	protein	103	Escherichia coli K-12	P45956 (AlphaFold model)
DNA (28-mer)	G	DNA	28	synthetic construct
DNA (45-mer)	H	DNA	61	synthetic construct
DNA (76-mer)	I	DNA	95	synthetic construct
DNA (61-mer)	J	DNA	62	synthetic construct
Integration host factor subunit alpha	K	protein	99	Escherichia coli S88	P0A6X7 (AlphaFold model)
Integration host factor subunit beta	L	protein	94	Escherichia coli S88	P0A6Y1 (AlphaFold model)

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

>5WFE_1 CRISPR-associated endonuclease Cas1 (chains A, B, C, D)
MTWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRV
SHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMF
ELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCI
SAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNP
GEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPAPPEDAQPVAIPLPVSLGDA
GHRSS

Sequence of entity 2 (E, F), FASTA

>5WFE_2 CRISPR-associated endoribonuclease Cas2 (chains E, F)
MSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAW
ATNTETGFEFQTFGLNRRTPVDLDGLRLVSFLPVGSSENLYFQ

Sequence of entity 3 (G), FASTA

>5WFE_3 DNA (28-MER) (chains G)
AAACACCAGAACGAGTAGTAAATTGGGC

Sequence of entity 4 (H), FASTA

>5WFE_4 DNA (45-MER) (chains H)
ATTTACTACTCGTTCTGGTGTTTCTCGTGTGTTCCCCGCGCCAGCGGGGATAAACCGAGC
A

Sequence of entity 5 (I), FASTA

>5WFE_5 DNA (76-MER) (chains I)
TGCTCGGTTTATCCCCGCTGGCGCGGGGAACACTCTAAACATAACCTATTATTAATTAAT
GATTTTTTAAGCCAGTCACAATCTACCAACTTTAT

Sequence of entity 6 (J), FASTA

>5WFE_6 DNA (61-MER) (chains J)
ATAAAGTTGGTAGATTGTGACTGGCTTAAAAAATCATTAATTAATAATAGGTTATGTTTA
GA

Sequence of entity 7 (K), FASTA

>5WFE_7 Integration host factor subunit alpha (chains K)
MALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQR
PGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPKDE

Sequence of entity 8 (L), FASTA

>5WFE_8 Integration host factor subunit beta (chains L)
MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRT
GRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG

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
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…

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