5H9E: E. coli Cascade

Crystal structure of E. coli Cascade bound to a PAM-containing dsDNA target (32-nt spacer) at 3.20 angstrom resolution. Determined by X-ray diffraction at 3.21 Å resolution. Released 17 Feb 2016.

Method: X-ray diffraction
Resolution: 3.21 Å
Organisms: Escherichia coli (strain K12), Escherichia coli
Chains: 14
Atoms: 27,217
Mol. weight: 435 kDa
Ligands: ZN
Released: 17 Feb 2016

Explore 5H9E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5H9E contains 171 α-helices and 166 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: 24 helices, 23 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	77-90	14
α-helix	111	1
β-strand	112-113	2	2
α-helix	114-117	4
α-helix	125-130	6
α-helix	132	1
β-strand	139-140	2	3
α-helix	141-153	13
α-helix	156-157	2
β-strand	162	1	4
β-strand	173-176	4	5
α-helix	181-187	7
α-helix	192-198	7
β-strand	206	1	6
α-helix	214-216	3
β-strand	220-222	3	7
α-helix	223-225	3
β-strand	226	1	6
α-helix	228-232	5
β-strand	238-241	4	2
α-helix	242-243	2
β-strand	245	1	3
β-strand	248-249	2	8
β-strand	256-257	2	8
β-strand	260-261	2	3
β-strand	263-267	5	2
β-strand	269	1	4
β-strand	272-274	3	7
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	345-352	8	5
β-strand	357-363	7	5
α-helix	376-405	30
α-helix	415-437	23
α-helix	443-466	24
α-helix	467-469	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: 11 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	52-66	15
β-strand	73-74	2	11
α-helix	87-94	8
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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	20	1	14
α-helix	25	1
β-strand	26	1	14
α-helix	27	1
β-strand	28-31	4	15
β-strand	34-37	4	15
β-strand	38-39	2	13
α-helix	41-49	9
α-helix	52-57	6
β-strand	63-67	5	16
α-helix	68-76	9
α-helix	85-96	12
β-strand	107-114	8	16
α-helix	116-132	17
α-helix	136-144	9
α-helix	148-153	6
α-helix	158-163	6
β-strand	165	1	17
α-helix	172-175	4
β-strand	178	1	17
β-strand	184	1	12
α-helix	185-186	2
β-strand	187-189	3	13
β-strand	222-225	4	13
β-strand	228-231	4	12
α-helix	232-238	7
α-helix	244-260	17
β-strand	278-280	3	13
β-strand	281-284	4	12
α-helix	291-294	4
α-helix	305-322	18
β-strand	331-333	3	13
α-helix	350-358	9

Chain E: 19 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	18
β-strand	12	1	19
β-strand	16	1	20
β-strand	20	1	21
β-strand	26	1	21
β-strand	28-31	4	22
β-strand	34-37	4	22
β-strand	38-39	2	23
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	24
α-helix	68-78	11
α-helix	85-96	12
β-strand	107-114	8	24
α-helix	116-131	16
α-helix	136-145	10
α-helix	148-153	6
α-helix	158-163	6
β-strand	165	1	25
α-helix	172-175	4
β-strand	178	1	25
β-strand	184	1	18
α-helix	185-186	2
β-strand	187-189	3	23
β-strand	196-202	7	26
β-strand	213-219	7	26
β-strand	220	1	20
β-strand	223	1	19
β-strand	224-225	2	23
β-strand	226-231	6	18
α-helix	233-238	6
α-helix	244-258	15
α-helix	267-270	4
α-helix	274-276	3
β-strand	278	1	27
β-strand	279-284	6	18
α-helix	291-294	4
α-helix	297-300	4
α-helix	305-322	18
β-strand	333	1	27
α-helix	350-358	9

Chain F: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	28
β-strand	20	1	29
α-helix	25	1
β-strand	26	1	29
α-helix	27	1
β-strand	28-31	4	30
β-strand	34-37	4	30
β-strand	38-39	2	28
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	31
α-helix	68-78	11
α-helix	85-96	12
β-strand	107-114	8	31
α-helix	116-131	16
α-helix	136-144	9
α-helix	148-152	5
α-helix	154-156	3
α-helix	158-163	6
β-strand	165	1	32
α-helix	172-175	4
β-strand	178	1	32
β-strand	184	1	28
α-helix	185-186	2
β-strand	187-189	3	28
β-strand	196-202	7	33
β-strand	213-219	7	33
β-strand	220-231	12	28
α-helix	233-238	6
α-helix	244-260	17
α-helix	267-270	4
α-helix	274-276	3
β-strand	278-284	7	28
α-helix	291-294	4
α-helix	305-322	18
β-strand	329-333	5	28
β-strand	344-347	4	28
α-helix	350-358	9

Chain G: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	34
β-strand	20	1	35
α-helix	25	1
β-strand	26	1	35
α-helix	27	1
β-strand	28-31	4	36
β-strand	34-37	4	36
β-strand	38-39	2	34
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	37
α-helix	68-78	11
α-helix	85-96	12
β-strand	107-114	8	37
α-helix	116-131	16
α-helix	136-144	9
α-helix	147-155	9
α-helix	158-163	6
β-strand	165	1	38
α-helix	172-175	4
β-strand	178	1	38
β-strand	182-184	3	34
β-strand	187-189	3	34
β-strand	196-202	7	39
β-strand	213-219	7	39
β-strand	220-231	12	34
α-helix	233-238	6
α-helix	244-260	17
α-helix	274-276	3
β-strand	278-284	7	34
α-helix	291-294	4
α-helix	297-300	4
α-helix	305-322	18
β-strand	330-333	4	34
β-strand	345-347	3	34
α-helix	350-358	9

Chain H: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	40
β-strand	20	1	41
α-helix	25	1
β-strand	26	1	41
α-helix	27	1
β-strand	28-31	4	42
β-strand	34-37	4	42
β-strand	38-39	2	40
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	43
α-helix	68-78	11
α-helix	85-96	12
β-strand	107-114	8	43
α-helix	116-131	16
α-helix	136-144	9
α-helix	148-154	7
α-helix	158-163	6
β-strand	165	1	44
α-helix	172-175	4
β-strand	178	1	44
β-strand	184	1	40
β-strand	187-189	3	40
β-strand	196-202	7	45
β-strand	213-219	7	45
β-strand	220-231	12	40
α-helix	233-238	6
α-helix	244-260	17
β-strand	278-284	7	40
α-helix	291-293	3
α-helix	297-300	4
α-helix	305-323	19
β-strand	329-333	5	40
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	182	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 (47-MER) Non-target	M	DNA	47	Escherichia coli
DNA (47-MER) Target	N	DNA	47	Escherichia coli
CRISPR system Cascade subunit CasE	K	protein	199	Escherichia coli (strain K12)	Q46897

Sequence of entity 1 (A), FASTA

>5H9E_1 CRISPR system Cascade subunit CasA (chains A)
MNLLIDNWIPVRPRNGGKVQIINLQSLYCSRDQWRLSLPRDDMELAALALLVCIGQIIAP
AKDDVEFRHRIMNPLTEDEFQQLIAPWIDMFYLNHAEHPFMQTKGVKANDVTPMEKLLAG
VSGATNCAFVNQPGQGEALCGGCTAIALFNQANQAPGFGGGFKSGLRGGTPVTTFVRGID
LRSTVLLNVLTLPRLQKQFPNESHTENQPTWIKPIKSNESIPASSIGFVRGLFWQPAHIE
LCDPIGIGKCSCCGQESNLRYTGFLKEKFTFTVNGLWPHPHSPCLVTVKKGEVEEKFLAF
TTSAPSWTQISRVVVDKIIQNENGNRVAAVVNQFRNIAPQSPLELIMGGYRNNQASILER
RHDVLMFNQGWQQYGNVINEIVTVGLGYKTALRKALYTFAEGFKNKDFKGAGVSVHETAE
RHFYRQSELLIPDVLANVNFSQADEVIADLRDKLHQLCEMLFNQSVAPYAHHPKLISTLA
LARATLYKHLRELKPQGGPSNG

Sequence of entity 2 (B, C), FASTA

>5H9E_2 CRISPR system Cascade subunit CasB (chains B, C)
MASHHHHHHGALEVLFQGPGYQMADEIDAMALYRAWQQLDNGSCAQIRRVSEPDELRDIP
AFYRLVQPFGWENPRHQQALLRMVFCLSAGKNVIRHQDKKSEQTTGISLGRALANSGRIN
ERRIFQLIRADRTADMVQLRRLLTHAEPVLDWPLMARMLTWWGKRERQQLLEDFVLTTNK
NA

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

>5H9E_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

>5H9E_4 CRISPR system Cascade subunit CasD (chains J)
MRSYLILRLAGPMQAWGQPTFEGTRPTGRFPTRSGLLGLLGACLGIQRDDTSSLQALSES
VQFAVRCDELILDDRRVSVTGLRDYHTVLGAREDYRGLKSHETIQTWREYLCDASFTVAL
WLTPHATMVISELEKAVLKPRYTPYLGRRSCPLTHPLFLGTCQASDPQKALLNYEPVGGD
IYSEESVTGHHLKFTARDEPMITLPRQFASREWYVIKGGMDVSQ

Sequence of entity 5 (L), FASTA

>5H9E_5 crRNA (61-MER) (chains L)
AUAAACCGACGGUAUUGUUCAGAUCCUGGCUUGCCAACAGGAGUUCCCCGCGCCAGCGGG
X

Sequence of entity 6 (M), FASTA

>5H9E_6 DNA (47-MER) Non-target (chains M)
GTGCAGTGCTCGATGTTTTATTTATTTTATTTATTATTTATTTTATA

Sequence of entity 7 (N), FASTA

>5H9E_7 DNA (47-MER) Target (chains N)
CTGTTGGCAAGCCAGGATCTGAACAATACCGTCATCGAGCACTGCAC

Sequence of entity 8 (K), FASTA

>5H9E_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:

5H9F 2.45 Å, Crystal structure of E. coli Cascade bound to a PAM-containing dsDNA target at 2.45…
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…
4TVX 3.24 Å, Crystal structure of the E. coli CRISPR RNA-guided surveillance complex, Cascade

Browse structure collections

About this viewer

MolViewer shows 5H9E directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.