4QYZ: CRISPR RNA-guided surveillance complex, Cascade

Crystal structure of a CRISPR RNA-guided surveillance complex, Cascade, bound to a ssDNA target. Determined by X-ray diffraction at 3.03 Å resolution. Released 3 Sept 2014.

Method: X-ray diffraction
Resolution: 3.03 Å
Organisms: Escherichia coli, Enterobacteria phage lambda
Chains: 13
Atoms: 26,543
Mol. weight: 413.4 kDa
Ligands: ZN
Released: 3 Sept 2014

Explore 4QYZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4QYZ contains 153 α-helices and 153 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: 21 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	7-11	5	2
β-strand	12-13	2	3
β-strand	20-23	4	2
α-helix	24-29	6
β-strand	34-35	2	3
α-helix	41-58	18
α-helix	64-72	9
α-helix	74-76	3
α-helix	77-90	14
β-strand	92	1	1
α-helix	115-118	4
β-strand	139	1	4
α-helix	141-153	13
β-strand	162	1	5
β-strand	171	1	6
β-strand	173-176	4	7
α-helix	181-187	7
α-helix	192-198	7
β-strand	220-222	3	8
α-helix	223-225	3
α-helix	228-232	5
β-strand	238-240	3	9
α-helix	242-244	3
β-strand	249	1	10
β-strand	256	1	10
β-strand	261	1	4
β-strand	265-267	3	9
β-strand	269	1	5
β-strand	272-274	3	8
β-strand	284-288	5	11
β-strand	293-297	5	11
β-strand	299	1	6
α-helix	306-310	5
α-helix	311-314	4
β-strand	317	1	11
β-strand	324-325	2	11
α-helix	329-337	9
β-strand	343-350	8	7
β-strand	360-367	8	7
α-helix	375-405	31
α-helix	411-414	4
α-helix	415-437	23
α-helix	445-470	26
α-helix	473-475	3
α-helix	476-492	17

Chain B: 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	55-65	11
β-strand	73-74	2	12
α-helix	87-94	8
α-helix	99-107	9
α-helix	110-124	15
β-strand	127-128	2	12
α-helix	130-138	9
α-helix	143-158	16

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	13
α-helix	87-94	8
α-helix	99-107	9
α-helix	110-124	15
β-strand	127-128	2	13
α-helix	130-138	9
α-helix	142-158	17

Chain D: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	14
β-strand	20	1	15
β-strand	26	1	15
α-helix	27	1
β-strand	28-30	3	16
β-strand	35-37	3	16
β-strand	38-39	2	14
α-helix	41-50	10
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	17
α-helix	68-79	12
α-helix	85-96	12
β-strand	107-114	8	17
α-helix	116-131	16
α-helix	136-144	9
α-helix	147-156	10
α-helix	160-163	4
β-strand	165	1	18
α-helix	171-174	4
β-strand	178	1	18
β-strand	182-184	3	14
α-helix	185-186	2
β-strand	187-189	3	14
β-strand	222-231	10	14
α-helix	232-238	7
α-helix	244-260	17
β-strand	278-284	7	14
α-helix	291-294	4
α-helix	297-300	4
α-helix	305-322	18
β-strand	328-332	5	14
β-strand	347	1	14
α-helix	350-358	9

Chain E: 18 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	19
β-strand	20	1	20
β-strand	26	1	20
β-strand	27-30	4	19
β-strand	35-39	5	19
α-helix	41-50	10
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	21
α-helix	68-79	12
α-helix	85-96	12
β-strand	107-114	8	21
α-helix	116-132	17
α-helix	136-145	10
α-helix	147-152	6
α-helix	153-155	3
α-helix	158-163	6
β-strand	165	1	22
β-strand	178	1	22
β-strand	182-184	3	19
β-strand	187-189	3	19
β-strand	196-202	7	23
β-strand	213-219	7	23
β-strand	220-231	12	19
α-helix	232-238	7
α-helix	244-260	17
α-helix	267-270	4
β-strand	276-284	9	19
α-helix	291-294	4
α-helix	297-300	4
β-strand	301	1	24
β-strand	303	1	24
α-helix	305-322	18
β-strand	329-333	5	19
α-helix	339-341	3
β-strand	345-347	3	19
α-helix	350-358	9

Chain F: 16 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	25
β-strand	20	1	26
β-strand	26	1	26
β-strand	28-31	4	27
β-strand	34-37	4	27
β-strand	38-39	2	25
α-helix	41-50	10
α-helix	52-57	6
β-strand	63-67	5	28
α-helix	68-82	15
α-helix	85-96	12
β-strand	107-114	8	28
α-helix	116-131	16
α-helix	136-145	10
α-helix	147-156	10
α-helix	158-163	6
β-strand	165	1	29
β-strand	178	1	29
β-strand	182-189	8	25
α-helix	194-195	2
β-strand	196-203	8	30
β-strand	211-219	9	30
β-strand	220-231	12	25
α-helix	232-238	7
α-helix	244-260	17
α-helix	267-270	4
β-strand	276-284	9	25
α-helix	290-294	5
α-helix	297-300	4
β-strand	301	1	31
β-strand	303	1	31
α-helix	305-322	18
β-strand	329-333	5	25
β-strand	345-347	3	25
α-helix	350-358	9

Chain G: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	32
β-strand	20	1	33
β-strand	26	1	33
β-strand	27	1	32
β-strand	30-31	2	34
β-strand	34-35	2	34
β-strand	38-39	2	32
α-helix	41-50	10
α-helix	52-57	6
β-strand	63-67	5	35
α-helix	68-79	12
α-helix	85-96	12
β-strand	107-114	8	35
α-helix	116-131	16
α-helix	136-145	10
α-helix	147-154	8
α-helix	158-163	6
β-strand	165	1	36
β-strand	178	1	36
β-strand	182-189	8	32
α-helix	194-195	2
β-strand	196-203	8	37
β-strand	211-219	9	37
β-strand	220-231	12	32
α-helix	232-238	7
α-helix	244-260	17
α-helix	267-270	4
β-strand	278-284	7	32
α-helix	290-294	5
α-helix	297-300	4
α-helix	305-322	18
β-strand	329-333	5	32
β-strand	345-346	2	32
α-helix	347	1
α-helix	350-358	9

Chain H: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	38
β-strand	20	1	39
β-strand	26	1	39
β-strand	27-31	5	38
β-strand	34-39	6	38
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	40
α-helix	68-79	12
α-helix	85-96	12
β-strand	107-114	8	40
α-helix	116-131	16
α-helix	136-145	10
α-helix	148-154	7
α-helix	158-163	6
β-strand	165	1	41
α-helix	172-175	4
β-strand	178	1	41
β-strand	182-189	8	38
β-strand	196-202	7	42
β-strand	213-219	7	42
β-strand	220-231	12	38
α-helix	232-238	7
α-helix	244-260	17
α-helix	267-270	4
β-strand	276-284	9	38
α-helix	290-294	5
α-helix	297-300	4
α-helix	305-322	18
β-strand	329-333	5	38
β-strand	345-347	3	38
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	Q46901 (AlphaFold model)
CRISPR system Cascade subunit CasB	B, C	protein	160	Escherichia coli	P76632 (AlphaFold model)
CRISPR system Cascade subunit CasC	D, E, F, G, H, I	protein	363	Escherichia coli	Q46899 (AlphaFold model)
CRISPR system Cascade subunit CasD	J	protein	224	Escherichia coli	Q46898 (AlphaFold model)
CRISPR system Cascade subunit CasE	K	protein	199	Escherichia coli	Q46897
RNA (55-mer)	L	RNA	61	Escherichia coli
DNA (33-mer)	M	DNA	40	Enterobacteria phage lambda

Sequence of entity 1 (A), FASTA

>4QYZ_1 CRISPR system Cascade subunit CasA (chains A)
MNLLIDNWIPVRPRNGGKVQIINLQSLYCSRDQWRLSLPRDDMELAALALLVCIGQIIAP
AKDDVEFRHRIMNPLTEDEFQQLIAPWIDMFYLNHAEHPFMQTKGVKANDVTPMEKLLAG
VSGATNCAFVNQPGQGEALCGGCTAIALFNQANQAPGFGGGFKSGLRGGTPVTTFVRGID
LRSTVLLNVLTLPRLQKQFPNESHTENQPTWIKPIKSNESIPASSIGFVRGLFWQPAHIE
LCDPIGIGKCSCCGQESNLRYTGFLKEKFTFTVNGLWPHPHSPCLVTVKKGEVEEKFLAF
TTSAPSWTQISRVVVDKIIQNENGNRVAAVVNQFRNIAPQSPLELIMGGYRNNQASILER
RHDVLMFNQGWQQYGNVINEIVTVGLGYKTALRKALYTFAEGFKNKDFKGAGVSVHETAE
RHFYRQSELLIPDVLANVNFSQADEVIADLRDKLHQLCEMLFNQSVAPYAHHPKLISTLA
LARATLYKHLRELKPQGGPSNG

Sequence of entity 2 (B, C), FASTA

>4QYZ_2 CRISPR system Cascade subunit CasB (chains B, C)
MADEIDAMALYRAWQQLDNGSCAQIRRVSEPDELRDIPAFYRLVQPFGWENPRHQQALLR
MVFCLSAGKNVIRHQDKKSEQTTGISLGRALANSGRINERRIFQLIRADRTADMVQLRRL
LTHAEPVLDWPLMARMLTWWGKRERQQLLEDFVLTTNKNA

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

>4QYZ_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

>4QYZ_4 CRISPR system Cascade subunit CasD (chains J)
MRSYLILRLAGPMQAWGQPTFEGTRPTGRFPTRSGLLGLLGACLGIQRDDTSSLQALSES
VQFAVRCDELILDDRRVSVTGLRDYHTVLGAREDYRGLKSHETIQTWREYLCDASFTVAL
WLTPHATMVISELEKAVLKPRYTPYLGRRSCPLTHPLFLGTCQASDPQKALLNYEPVGGD
IYSEESVTGHHLKFTARDEPMITLPRQFASREWYVIKGGMDVSQ

Sequence of entity 5 (K), FASTA

>4QYZ_5 CRISPR system Cascade subunit CasE (chains K)
MYLSKVIIARAWSRDLYQLHQGLWHLFPNRPDAARDFLFHVEKRNTPEGCHVLLQSAQMP
VSTAVATVIKTKQVEFQLQVGVPLYFRLRANPIKTILDNQKRLDSKGNIKRCRVPLIKEA
EQIAWLQRKLGNAARVEDVHPISERPQYFSGDGKSGKIQTVCFEGVLTINDAPALIDLVQ
QGIGPAKSMGCGLLSLAPL

Sequence of entity 6 (L), FASTA

>4QYZ_6 RNA (55-MER) (chains L)
AUAAACCGCCAGUGAUAAGUGGAAUGCCAUGUGGGCUGUCGAGUUCCCGGCGCCAGCCGG
G

Sequence of entity 7 (M), FASTA

>4QYZ_7 DNA (33-MER) (chains M)
AATCAGACAGCCCACATGGCATTCCACTTATCACTGGCAT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structural biology. Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target. Mulepati, S., Heroux, A., Bailey, S. Science (2014) 345:1479-1484. DOI 10.1126/science.1256996 · 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
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

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4QYZ is part of these collections:

CRISPR and genome editing

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