5CD4: CRISPR system Cascade subunit CasE

The Type IE CRISPR Cascade complex from E. coli, with two assemblies in the asymmetric unit arranged back-to-back. Determined by X-ray diffraction at 3.2 Å resolution. Released 26 Aug 2015.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Escherichia coli
Chains: 24
Atoms: 53,308
Mol. weight: 804.32 kDa
Ligands: ZN
Released: 26 Aug 2015

Explore 5CD4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5CD4 contains 364 α-helices and 319 β-strands across 22 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: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
α-helix	10-12	3
α-helix	16-24	9
β-strand	37-43	7	1
β-strand	49-56	8	1
β-strand	66-73	8	1
α-helix	78-79	2
β-strand	83-90	8	2
β-strand	93-97	5	3
β-strand	103	1	4
β-strand	109	1	4
β-strand	111-115	5	3
α-helix	119-130	12
α-helix	131-133	3
β-strand	134-149	16	2
β-strand	156-169	14	2
α-helix	172-181	10
α-helix	187-189	3
β-strand	194-198	5	2

Chain B: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	5
β-strand	20	1	6
β-strand	26	1	6
β-strand	28-31	4	7
β-strand	34-37	4	7
β-strand	38-39	2	5
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	8
α-helix	68-79	12
α-helix	85-96	12
β-strand	107-114	8	8
α-helix	116-125	10
α-helix	126-130	5
α-helix	133-135	3
α-helix	136-144	9
α-helix	148-152	5
α-helix	153-156	4
α-helix	158-163	6
β-strand	165	1	9
α-helix	172-175	4
β-strand	178	1	9
β-strand	182-184	3	5
α-helix	185-186	2
β-strand	187-189	3	5
α-helix	199-202	4
α-helix	203-206	4
α-helix	215-218	4
β-strand	222-231	10	5
α-helix	232-238	7
α-helix	244-260	17
β-strand	278-284	7	5
α-helix	291-294	4
α-helix	305-322	18
β-strand	329-332	4	5
β-strand	345-346	2	5
α-helix	350-358	9

Chain C: 20 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	10
β-strand	20	1	11
α-helix	25	1
β-strand	26	1	11
α-helix	27	1
β-strand	28-31	4	12
β-strand	34-37	4	12
β-strand	38-39	2	10
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	13
α-helix	68-78	11
α-helix	85-96	12
β-strand	107-114	8	13
α-helix	116-129	14
α-helix	133-135	3
α-helix	136-143	8
α-helix	147-152	6
α-helix	153-156	4
α-helix	158-163	6
β-strand	165	1	14
α-helix	172-175	4
β-strand	178	1	14
β-strand	182-184	3	10
α-helix	185-186	2
β-strand	187-189	3	10
β-strand	196-200	5	15
β-strand	215-219	5	15
β-strand	220-231	12	10
α-helix	232-238	7
α-helix	244-260	17
β-strand	278-284	7	10
α-helix	291-294	4
α-helix	305-322	18
β-strand	329-333	5	10
β-strand	345-346	2	10
α-helix	350-358	9

Chain D: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	16
β-strand	20	1	17
β-strand	26	1	17
β-strand	28-31	4	18
β-strand	34-37	4	18
β-strand	38-39	2	16
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	19
α-helix	68-78	11
α-helix	85-96	12
α-helix	99-100	2
β-strand	107-114	8	19
α-helix	116-132	17
α-helix	134-135	2
α-helix	136-143	8
α-helix	148-151	4
α-helix	152-155	4
α-helix	158-163	6
β-strand	165	1	20
α-helix	172-175	4
β-strand	178	1	20
β-strand	182-184	3	16
α-helix	185-186	2
β-strand	187-189	3	16
β-strand	196-202	7	21
β-strand	213-219	7	21
β-strand	220-231	12	16
α-helix	232-238	7
α-helix	244-260	17
α-helix	274-276	3
β-strand	278-284	7	16
α-helix	290-293	4
α-helix	297-300	4
α-helix	305-322	18
β-strand	329-333	5	16
β-strand	345-346	2	16
α-helix	350-358	9

Chain E: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	22
β-strand	20	1	23
β-strand	26	1	23
β-strand	28-31	4	24
β-strand	34-37	4	24
β-strand	38-39	2	22
α-helix	41-49	9
α-helix	52-57	6
α-helix	60-62	3
β-strand	63-67	5	25
α-helix	68-78	11
α-helix	85-95	11
β-strand	107-114	8	25
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	26
α-helix	172-175	4
β-strand	178	1	26
β-strand	182-184	3	22
α-helix	185-186	2
β-strand	187-189	3	22
β-strand	196-200	5	27
α-helix	211-213	3
β-strand	215-219	5	27
β-strand	220-231	12	22
α-helix	232-238	7
α-helix	244-260	17
β-strand	278-284	7	22
α-helix	291-294	4
α-helix	305-323	19
β-strand	329-333	5	22
β-strand	345-346	2	22
α-helix	350-358	9

Chain F: 18 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	68-79	12
α-helix	85-96	12
β-strand	107-114	8	31
α-helix	116-126	11
α-helix	136-145	10
α-helix	148-151	4
α-helix	152-156	5
α-helix	159-163	5
β-strand	165	1	32
α-helix	172-175	4
β-strand	178	1	32
β-strand	182-184	3	28
β-strand	187-189	3	28
β-strand	196-200	5	33
β-strand	215-219	5	33
β-strand	220-231	12	28
α-helix	232-238	7
α-helix	244-260	17
β-strand	278-284	7	28
α-helix	291-294	4
α-helix	305-323	19
β-strand	329-333	5	28
β-strand	344-347	4	28
α-helix	350-358	9

Chain G: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	34
β-strand	20	1	35
β-strand	26	1	35
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	68-71	4
α-helix	72-78	7
α-helix	85-96	12
α-helix	113-132	20
α-helix	136-142	7
α-helix	144-153	10
α-helix	157-163	7
α-helix	174-176	3
β-strand	182-184	3	34
α-helix	185-186	2
β-strand	187-189	3	34
β-strand	196-202	7	37
β-strand	213-219	7	37
β-strand	220-231	12	34
α-helix	232-237	6
α-helix	244-260	17
α-helix	274-276	3
β-strand	278-284	7	34
α-helix	291-294	4
α-helix	297-298	2
α-helix	305-322	18
β-strand	329-333	5	34
β-strand	344-347	4	34
α-helix	350-358	9

Chain H: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	38
β-strand	14	1	39
β-strand	24-25	2	39
α-helix	33-44	12
α-helix	51-60	10
β-strand	61-68	8	38
β-strand	70-72	3	40
β-strand	75-77	3	40
β-strand	80-89	10	39
β-strand	92	1	41
β-strand	100	1	41
β-strand	103-112	10	39
β-strand	115-122	8	38
α-helix	130-138	9
β-strand	158-164	7	38
α-helix	167-171	5
β-strand	181-183	3	38
β-strand	193-200	8	38
β-strand	208-216	9	38

13 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 CasE	A, M	protein	199	Escherichia coli	Q46897 (AlphaFold model)
CRISPR system Cascade subunit CasC	B, C, D, E, F, G, N, O, P, Q, R, S	protein	363	Escherichia coli	Q46899 (AlphaFold model)
CRISPR system Cascade subunit CasD	H, T	protein	224	Escherichia coli	Q46898 (AlphaFold model)
CRISPR system Cascade subunit CasA	I, U	protein	502	Escherichia coli	Q46901 (AlphaFold model)
CRISPR system Cascade subunit CasB	J, K, V, W	protein	165	Escherichia coli	P76632
crRNA	L, X	RNA	61	Escherichia coli

Sequence of entity 1 (A, M), FASTA

>5CD4_1 CRISPR system Cascade subunit CasE (chains A, M)
MYLSKVIIARAWSRDLYQLHQGLWHLFPNRPDAARDFLFHVEKRNTPEGCHVLLQSAQMP
VSTAVATVIKTKQVEFQLQVGVPLYFRLRANPIKTILDNQKRLDSKGNIKRCRVPLIKEA
EQIAWLQRKLGNAARVEDVHPISERPQYFSGDGKSGKIQTVCFEGVLTINDAPALIDLVQ
QGIGPAKSMGCGLLSLAPL

Sequence of entity 2 (B, C, D, E, F, G, N, O, P, Q, R, S), FASTA

>5CD4_2 CRISPR system Cascade subunit CasC (chains B, C, D, E, F, G, N, O, P, Q, R, S)
MSNFINIHVLISHSPSCLNRDDMNMQKDAIFGGKRRVRISSQSLKRAMRKSGYYAQNIGE
SSLRTIHLAQLRDVLRQKLGERFDQKIIDKTLALLSGKSVDEAEKISADAVTPWVVGEIA
WFCEQVAKAEADNLDDKKLLKVLKEDIAAIRVNLQQGVDIALSGRMATSGMMTELGKVDG
AMSIAHAITTHQVDSDIDWFTAVDDLQEQGSAHLGTQEFSSGVFYRYANINLAQLQENLG
GASREQALEIATHVVHMLATEVPGAKQRTYAAFNPADMVMVNFSDMPLSMANAFEKAVKA
KDGFLQPSIQAFNQYWDRVANGYGLNGAAAQFSLSDVDPITAQVKQMPTLEQLKSWVRNN
GEA

Sequence of entity 3 (H, T), FASTA

>5CD4_3 CRISPR system Cascade subunit CasD (chains H, T)
MRSYLILRLAGPMQAWGQPTFEGTRPTGRFPTRSGLLGLLGACLGIQRDDTSSLQALSES
VQFAVRCDELILDDRRVSVTGLRDYHTVLGAREDYRGLKSHETIQTWREYLCDASFTVAL
WLTPHATMVISELEKAVLKPRYTPYLGRRSCPLTHPLFLGTCQASDPQKALLNYEPVGGD
IYSEESVTGHHLKFTARDEPMITLPRQFASREWYVIKGGMDVSQ

Sequence of entity 4 (I, U), FASTA

>5CD4_4 CRISPR system Cascade subunit CasA (chains I, U)
MNLLIDNWIPVRPRNGGKVQIINLQSLYCSRDQWRLSLPRDDMELAALALLVCIGQIIAP
AKDDVEFRHRIMNPLTEDEFQQLIAPWIDMFYLNHAEHPFMQTKGVKANDVTPMEKLLAG
VSGATNCAFVNQPGQGEALCGGCTAIALFNQANQAPGFGGGFKSGLRGGTPVTTFVRGID
LRSTVLLNVLTLPRLQKQFPNESHTENQPTWIKPIKSNESIPASSIGFVRGLFWQPAHIE
LCDPIGIGKCSCCGQESNLRYTGFLKEKFTFTVNGLWPHPHSPCLVTVKKGEVEEKFLAF
TTSAPSWTQISRVVVDKIIQNENGNRVAAVVNQFRNIAPQSPLELIMGGYRNNQASILER
RHDVLMFNQGWQQYGNVINEIVTVGLGYKTALRKALYTFAEGFKNKDFKGAGVSVHETAE
RHFYRQSELLIPDVLANVNFSQADEVIADLRDKLHQLCEMLFNQSVAPYAHHPKLISTLA
LARATLYKHLRELKPQGGPSNG

Sequence of entity 5 (J, K, V, W), FASTA

>5CD4_5 CRISPR system Cascade subunit CasB (chains J, K, V, W)
GPGYQMADEIDAMALYRAWQQLDNGSCAQIRRVSEPDELRDIPAFYRLVQPFGWENPRHQ
QALLRMVFCLSAGKNVIRHQDKKSEQTTGISLGRALANSGRINERRIFQLIRADRTADMV
QLRRLLTHAEPVLDWPLMARMLTWWGKRERQQLLEDFVLTTNKNA

Sequence of entity 6 (L, X), FASTA

>5CD4_6 crRNA (chains L, X)
AUAAACCGACGGUAUUGUUCAGAUCCUGGCUUGCCAACAGGAGUUCCCCGCGCCAGCGGG
X

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli. van Erp, P.B., Jackson, R.N., Carter, J. et al. Nucleic Acids Res (2015) 43:8381-8391. DOI 10.1093/nar/gkv793 · PubMed

Other PDB entries of the same protein (UniProt Q46897 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4DZD 2.0 Å, Crystal structure of the CRISPR-associated protein Cas6e from Escherichia coli str. K-12
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…
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

About this viewer

MolViewer shows 5CD4 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.