5H9F: E. coli Cascade

Crystal structure of E. coli Cascade bound to a PAM-containing dsDNA target at 2.45 angstrom resolution. Determined by X-ray diffraction at 2.45 Å resolution. Released 17 Feb 2016.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Escherichia coli (strain K12), Escherichia coli
Chains: 14
Atoms: 28,930
Mol. weight: 426.15 kDa
Ligands: ZN
Released: 17 Feb 2016

Explore 5H9F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5H9F contains 184 α-helices and 158 β-strands across 11 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: 29 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	1
β-strand	20-22	3	1
α-helix	24-28	5
β-strand	34-36	3	1
α-helix	41-58	18
α-helix	64-72	9
α-helix	74-76	3
α-helix	77-84	8
α-helix	85-90	6
α-helix	111	1
β-strand	112	1	2
α-helix	113	1
α-helix	114-117	4
α-helix	127-130	4
α-helix	132	1
β-strand	139	1	3
α-helix	141-153	13
α-helix	156-157	2
α-helix	171-172	2
β-strand	173-176	4	4
α-helix	181-187	7
α-helix	192-198	7
β-strand	206	1	5
α-helix	214-216	3
β-strand	220-222	3	6
α-helix	223-225	3
β-strand	226	1	5
α-helix	228-232	5
β-strand	238-241	4	2
β-strand	245	1	7
β-strand	248-249	2	8
β-strand	256-257	2	8
β-strand	260	1	7
β-strand	261	1	3
β-strand	264-267	4	2
β-strand	272-274	3	6
β-strand	284-289	6	9
β-strand	292-297	6	9
α-helix	311-321	11
β-strand	325-326	2	9
α-helix	329-337	9
β-strand	345-353	9	4
β-strand	356-363	8	4
α-helix	376-405	30
α-helix	411-414	4
α-helix	415-428	14
α-helix	431-437	7
α-helix	443-466	24
α-helix	467-469	3
α-helix	473-475	3
α-helix	476-491	16

Chain B: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-16	10
α-helix	19-26	8
α-helix	31-36	6
α-helix	38-44	7
α-helix	45-47	3
α-helix	52-65	14
β-strand	73-74	2	10
α-helix	87-94	8
α-helix	99-106	8
α-helix	112-124	13
β-strand	127-128	2	10
α-helix	130-138	9
α-helix	142-158	17

Chain C: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-15	9
α-helix	19-26	8
α-helix	31-36	6
α-helix	38-44	7
α-helix	45-47	3
α-helix	52-54	3
α-helix	55-65	11
β-strand	73-74	2	11
α-helix	87-93	7
α-helix	99-107	9
α-helix	112-124	13
β-strand	127-128	2	11
α-helix	130-139	10
α-helix	142-155	14

Chain D: 17 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	12
β-strand	12-13	2	13
β-strand	20	1	14
β-strand	26	1	14
β-strand	28-31	4	15
β-strand	34-37	4	15
β-strand	38-39	2	16
α-helix	41-49	9
α-helix	52-57	6
β-strand	63-67	5	17
α-helix	68-76	9
α-helix	85-96	12
α-helix	99-100	2
β-strand	107-114	8	17
α-helix	116-132	17
α-helix	136-144	9
α-helix	148-151	4
α-helix	152-155	4
α-helix	158-163	6
β-strand	165	1	18
α-helix	172-175	4
β-strand	178	1	18
β-strand	182-184	3	12
α-helix	185-186	2
β-strand	187-189	3	16
β-strand	222-223	2	13
β-strand	224-225	2	16
β-strand	226-231	6	12
α-helix	232-238	7
α-helix	244-260	17
β-strand	278-284	7	12
α-helix	291-294	4
α-helix	305-322	18
β-strand	329-333	5	12
β-strand	345-347	3	12
α-helix	350-358	9

Chain E: 20 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	19
β-strand	20	1	20
β-strand	26	1	20
β-strand	28-31	4	21
β-strand	34-37	4	21
β-strand	38-39	2	19
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	22
α-helix	68-78	11
α-helix	85-96	12
β-strand	107-114	8	22
α-helix	116-131	16
α-helix	136-143	8
α-helix	148-151	4
α-helix	152-156	5
α-helix	158-163	6
β-strand	165	1	23
α-helix	172-175	4
β-strand	178	1	23
β-strand	182-184	3	19
α-helix	185-186	2
β-strand	187-189	3	19
β-strand	196-202	7	24
β-strand	213-219	7	24
β-strand	220-231	12	19
α-helix	232-238	7
α-helix	244-258	15
α-helix	267-270	4
α-helix	274-276	3
β-strand	278-284	7	19
α-helix	291-294	4
α-helix	297-300	4
α-helix	305-322	18
β-strand	329-333	5	19
β-strand	344-346	3	19
α-helix	350-358	9

Chain F: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	25
β-strand	20	1	26
α-helix	25	1
β-strand	26	1	26
α-helix	27	1
β-strand	28-31	4	27
β-strand	34-37	4	27
β-strand	38-39	2	25
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	28
α-helix	68-78	11
α-helix	85-96	12
β-strand	107-114	8	28
α-helix	116-131	16
α-helix	136-143	8
α-helix	148-151	4
α-helix	152-156	5
α-helix	158-163	6
β-strand	165	1	29
α-helix	172-175	4
β-strand	178	1	29
β-strand	182-184	3	25
α-helix	185-186	2
β-strand	187-189	3	25
β-strand	196-202	7	30
β-strand	213-219	7	30
β-strand	220-231	12	25
α-helix	232-238	7
α-helix	244-260	17
α-helix	267-270	4
β-strand	278-284	7	25
α-helix	291-294	4
α-helix	297-300	4
α-helix	305-322	18
β-strand	329-333	5	25
β-strand	345-347	3	25
α-helix	350-358	9

Chain G: 23 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	31
β-strand	20	1	32
α-helix	25	1
β-strand	26	1	32
α-helix	27	1
β-strand	28-31	4	33
β-strand	34-37	4	33
β-strand	38-39	2	31
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	34
α-helix	68-78	11
α-helix	85-96	12
β-strand	107-114	8	34
α-helix	116-131	16
α-helix	136-143	8
α-helix	144-146	3
α-helix	147-151	5
α-helix	152-155	4
α-helix	158-163	6
β-strand	165	1	35
α-helix	172-175	4
β-strand	178	1	35
β-strand	182-184	3	31
α-helix	185-186	2
β-strand	187-189	3	31
β-strand	196-202	7	36
β-strand	213-219	7	36
β-strand	220-231	12	31
α-helix	232-238	7
α-helix	244-260	17
α-helix	267-270	4
α-helix	274-276	3
β-strand	278-284	7	31
α-helix	291-294	4
α-helix	297-300	4
α-helix	305-322	18
β-strand	329-333	5	31
β-strand	345-347	3	31
α-helix	350-358	9

Chain H: 22 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	37
β-strand	20	1	38
α-helix	25	1
β-strand	26	1	38
α-helix	27	1
β-strand	28-31	4	39
β-strand	34-37	4	39
β-strand	38-39	2	37
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	40
α-helix	68-78	11
α-helix	85-96	12
β-strand	107-114	8	40
α-helix	116-131	16
α-helix	136-143	8
α-helix	148-151	4
α-helix	152-156	5
α-helix	158-163	6
β-strand	165	1	41
α-helix	172-175	4
β-strand	178	1	41
β-strand	182-184	3	37
α-helix	185-186	2
β-strand	187-189	3	37
β-strand	196-202	7	42
β-strand	213-219	7	42
β-strand	220-231	12	37
α-helix	232-238	7
α-helix	244-260	17
α-helix	267-270	4
α-helix	274-276	3
β-strand	278-284	7	37
α-helix	291-293	3
α-helix	297-300	4
α-helix	305-323	19
β-strand	329-333	5	37
β-strand	345-347	3	37
α-helix	350-358	9

3 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 system Cascade subunit CasA	A	protein	502	Escherichia coli (strain K12)	Q46901 (AlphaFold model)
CRISPR system Cascade subunit CasB	B, C	protein	165	Escherichia coli (strain K12)	P76632 (AlphaFold model)
CRISPR system Cascade subunit CasC	D, E, F, G, H, I	protein	363	Escherichia coli (strain K12)	Q46899 (AlphaFold model)
CRISPR system Cascade subunit CasD	J	protein	224	Escherichia coli (strain K12)	Q46898 (AlphaFold model)
crRNA (61-MER)	L	RNA	61	Escherichia coli
DNA (28-MER) Non-target	M	DNA	28	Escherichia coli
DNA (50-MER) Target	N	DNA	50	Escherichia coli
CRISPR system Cascade subunit CasE	K	protein	199	Escherichia coli (strain K12)	Q46897

Sequence of entity 1 (A), FASTA

>5H9F_1 CRISPR system Cascade subunit CasA (chains A)
MNLLIDNWIPVRPRNGGKVQIINLQSLYCSRDQWRLSLPRDDMELAALALLVCIGQIIAP
AKDDVEFRHRIMNPLTEDEFQQLIAPWIDMFYLNHAEHPFMQTKGVKANDVTPMEKLLAG
VSGATNCAFVNQPGQGEALCGGCTAIALFNQANQAPGFGGGFKSGLRGGTPVTTFVRGID
LRSTVLLNVLTLPRLQKQFPNESHTENQPTWIKPIKSNESIPASSIGFVRGLFWQPAHIE
LCDPIGIGKCSCCGQESNLRYTGFLKEKFTFTVNGLWPHPHSPCLVTVKKGEVEEKFLAF
TTSAPSWTQISRVVVDKIIQNENGNRVAAVVNQFRNIAPQSPLELIMGGYRNNQASILER
RHDVLMFNQGWQQYGNVINEIVTVGLGYKTALRKALYTFAEGFKNKDFKGAGVSVHETAE
RHFYRQSELLIPDVLANVNFSQADEVIADLRDKLHQLCEMLFNQSVAPYAHHPKLISTLA
LARATLYKHLRELKPQGGPSNG

Sequence of entity 2 (B, C), FASTA

>5H9F_2 CRISPR system Cascade subunit CasB (chains B, C)
GPGYQMADEIDAMALYRAWQQLDNGSCAQIRRVSEPDELRDIPAFYRLVQPFGWENPRHQ
QALLRMVFCLSAGKNVIRHQDKKSEQTTGISLGRALANSGRINERRIFQLIRADRTADMV
QLRRLLTHAEPVLDWPLMARMLTWWGKRERQQLLEDFVLTTNKNA

Sequence of entity 3 (D, E, F, G, H, I), FASTA

>5H9F_3 CRISPR system Cascade subunit CasC (chains D, E, F, G, H, I)
MSNFINIHVLISHSPSCLNRDDMNMQKDAIFGGKRRVRISSQSLKRAMRKSGYYAQNIGE
SSLRTIHLAQLRDVLRQKLGERFDQKIIDKTLALLSGKSVDEAEKISADAVTPWVVGEIA
WFCEQVAKAEADNLDDKKLLKVLKEDIAAIRVNLQQGVDIALSGRMATSGMMTELGKVDG
AMSIAHAITTHQVDSDIDWFTAVDDLQEQGSAHLGTQEFSSGVFYRYANINLAQLQENLG
GASREQALEIATHVVHMLATEVPGAKQRTYAAFNPADMVMVNFSDMPLSMANAFEKAVKA
KDGFLQPSIQAFNQYWDRVANGYGLNGAAAQFSLSDVDPITAQVKQMPTLEQLKSWVRNN
GEA

Sequence of entity 4 (J), FASTA

>5H9F_4 CRISPR system Cascade subunit CasD (chains J)
MRSYLILRLAGPMQAWGQPTFEGTRPTGRFPTRSGLLGLLGACLGIQRDDTSSLQALSES
VQFAVRCDELILDDRRVSVTGLRDYHTVLGAREDYRGLKSHETIQTWREYLCDASFTVAL
WLTPHATMVISELEKAVLKPRYTPYLGRRSCPLTHPLFLGTCQASDPQKALLNYEPVGGD
IYSEESVTGHHLKFTARDEPMITLPRQFASREWYVIKGGMDVSQ

Sequence of entity 5 (L), FASTA

>5H9F_5 crRNA (61-MER) (chains L)
AUAAACCGACGGUAUUGUUCAGAUCCUGGCUUGCCAACAGGAGUUCCCCGCGCCAGCGGG
X

Sequence of entity 6 (M), FASTA

>5H9F_6 DNA (28-MER) Non-target (chains M)
TCTGTGCAGTGCTCGATGTTTTATTTAT

Sequence of entity 7 (N), FASTA

>5H9F_7 DNA (50-MER) Target (chains N)
CTGTTGGCAAGCCAGGATCTGAACAATACCGTCATCGAGCACTGCACAGA

Sequence of entity 8 (K), FASTA

>5H9F_8 CRISPR system Cascade subunit CasE (chains K)
MYLSKVIIARAWSRDLYQLHQGLWHLFPNRPDAARDFLFHVEKRNTPEGCHVLLQSAQMP
VSTAVATVIKTKQVEFQLQVGVPLYFRLRANPIKTILDNQKRLDSKGNIKRCRVPLIKEA
EQIAWLQRKLGNAARVEDVHPISERPQYFSGDGKSGKIQTVCFEGVLTINDAPALIDLVQ
QGIGPAKSMGCGLLSLAPL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli. Hayes, R.P., Xiao, Y., Ding, F. et al. Nature (2016) 530:499-503. DOI 10.1038/nature16995 · PubMed

Other PDB entries of the same protein (UniProt Q46901 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4U7U 3.0 Å, Crystal structure of RNA-guided immune Cascade complex from E.coli
4QYZ 3.03 Å, Crystal structure of a CRISPR RNA-guided surveillance complex, Cascade, bound to a ssDNA…
5CD4 3.2 Å, The Type IE CRISPR Cascade complex from E. coli, with two assemblies in the asymmetric…
5H9E 3.21 Å, Crystal structure of E. coli Cascade bound to a PAM-containing dsDNA target (32-nt…
4TVX 3.24 Å, Crystal structure of the E. coli CRISPR RNA-guided surveillance complex, Cascade

Browse structure collections

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