1LVC: Adenylyl cyclase domain of anthrax edema factor

Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 2' deoxy, 3' anthraniloyl ATP. Determined by X-ray diffraction at 3.6 Å resolution. Released 4 Dec 2002.

Method: X-ray diffraction
Resolution: 3.6 Å
Organisms: Bacillus anthracis, Homo sapiens
Chains: 6
Atoms: 15,302
Mol. weight: 228.97 kDa
Ligands: CA, DOT, YB
Released: 4 Dec 2002

Explore 1LVC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1LVC contains 102 α-helices and 83 β-strands across 6 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: 25 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	296-297	2	1
α-helix	298-305	8
α-helix	309-321	13
β-strand	324-328	5	1
α-helix	333-340	8
α-helix	343	1
β-strand	344-345	2	2
α-helix	346	1
α-helix	352-355	4
β-strand	363	1	2
β-strand	365	1	3
α-helix	368-370	3
α-helix	377-392	16
β-strand	395	1	3
β-strand	398-402	5	3
β-strand	404	1	4
α-helix	407-416	10
β-strand	420-426	7	5
β-strand	431-436	6	5
β-strand	442-447	6	5
β-strand	452	1	4
β-strand	453-457	5	5
β-strand	472-473	2	5
α-helix	474	1
β-strand	475-481	7	3
β-strand	484-487	4	3
β-strand	488-489	2	2
β-strand	494-499	6	1
β-strand	500	1	6
α-helix	501-505	5
α-helix	512-517	6
α-helix	523-533	11
α-helix	534-538	5
β-strand	541-542	2	7
β-strand	548-549	2	7
α-helix	551-567	17
α-helix	580-582	3
β-strand	593-596	4	1
β-strand	602-605	4	1
α-helix	608-618	11
β-strand	624	1	6
α-helix	648-653	6
α-helix	660-668	9
α-helix	696-704	9
α-helix	707-709	3
α-helix	714-736	23
α-helix	745-767	23
α-helix	774-778	5
α-helix	788-796	9

Chain B: 20 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	297	1	8
α-helix	299-305	7
α-helix	309-321	13
β-strand	324-328	5	8
α-helix	333-340	8
β-strand	344-345	2	9
β-strand	365	1	10
α-helix	368-370	3
α-helix	377-392	16
β-strand	398-402	5	10
β-strand	404	1	11
α-helix	409-415	7
β-strand	420-426	7	12
β-strand	431-436	6	12
β-strand	442-447	6	12
β-strand	452	1	11
β-strand	453-457	5	12
α-helix	458	1
β-strand	472-473	2	12
β-strand	475-481	7	10
β-strand	484-487	4	10
β-strand	488-489	2	9
β-strand	494-499	6	8
β-strand	500	1	13
α-helix	502-505	4
α-helix	510-517	8
α-helix	525-533	9
α-helix	534-538	5
β-strand	541-542	2	14
β-strand	548-549	2	14
α-helix	551-565	15
α-helix	580-582	3
β-strand	594-596	3	8
β-strand	602-604	3	8
α-helix	608-614	7
α-helix	615-619	5
β-strand	624	1	13
β-strand	635	1	15
β-strand	642	1	15
α-helix	648-651	4
α-helix	714-727	14
α-helix	728-730	3
α-helix	743-764	22
α-helix	786-790	5

Chain C: 27 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	298-305	8
α-helix	309-321	13
β-strand	324-328	5	16
α-helix	329-330	2
α-helix	333-340	8
α-helix	343	1
β-strand	344-345	2	17
α-helix	346	1
α-helix	352-355	4
β-strand	363	1	17
β-strand	365	1	18
α-helix	368-370	3
α-helix	377-392	16
β-strand	395	1	18
β-strand	398-402	5	18
β-strand	404	1	19
α-helix	407-416	10
β-strand	420-426	7	20
β-strand	431-436	6	20
β-strand	442-447	6	20
β-strand	452	1	19
β-strand	453-457	5	20
β-strand	472-473	2	20
α-helix	474	1
β-strand	475-481	7	18
β-strand	484-487	4	18
β-strand	488-489	2	17
β-strand	494-499	6	16
β-strand	500	1	21
α-helix	501-505	5
α-helix	512-515	4
α-helix	522-533	12
α-helix	534-538	5
β-strand	541-543	3	22
β-strand	547-549	3	22
α-helix	551-567	17
α-helix	580-582	3
β-strand	593-596	4	16
β-strand	602-605	4	16
α-helix	608-618	11
β-strand	624	1	21
α-helix	648-651	4
α-helix	653-655	3
α-helix	661-669	9
α-helix	696-704	9
α-helix	707-709	3
α-helix	714-736	23
α-helix	745-765	21
α-helix	774-778	5
α-helix	787-796	10

Chain D: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	12-16	5
β-strand	27-28	2	23
α-helix	32-36	5
α-helix	45-55	11
β-strand	62-63	2	23
α-helix	65-75	11
α-helix	78-81	4
α-helix	82-92	11
β-strand	99-100	2	24
α-helix	102-110	9
α-helix	118-128	11
β-strand	136-137	2	24
α-helix	138-143	6

Chains E and F: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	12-16	5
β-strand	27-28	2	25
α-helix	32-36	5
α-helix	45-55	11
β-strand	62-63	2	25
α-helix	65-75	11
α-helix	78-81	4
α-helix	82-92	11
β-strand	99-100	2	26
α-helix	102-110	9
α-helix	118-128	11
β-strand	136-137	2	26
α-helix	138-146	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
calmodulin-sensitive adenylate cyclase	A, B, C	protein	510	Bacillus anthracis	P40136 (AlphaFold model)
calmodulin	D, E, F	protein	149	Homo sapiens	P0DP23 (AlphaFold model)

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

>1LVC_1 calmodulin-sensitive adenylate cyclase (chains A, B, C)
DRIDVLKGEKALKASGLVPEHADAFKKIARELNTYILFRPVNKLATNLIKSGVATKGLNV
HGKSSDWGPVAGYIPFDQDLSKKHGQQLAVEKGNLENKKSITEHEGEIGKIPLKLDHLRI
EELKENGIILKGKKEIDNGKKYYLLESNNQVYEFRISDENNEVQYKTKEGKITVLGEKFN
WRNIEVMAKNVEGVLKPLTADYDLFALAPSLTEIKKQIPQKEWDKVVNTPNSLEKQKGVT
NLLIKYGIERKPDSTKGTLSNWQKQMLDRLNEAVKYTGYTGGDVVNHGTEQDNEEFPEKD
NEIFIINPEGEFILTKNWEMTGRFIEKNITGKDYLYYFNRSYNKIAPGNKAYIEWTDPIT
KAKINTIPTSAEFIKNLSSIRRSSNVGVYKDSGDKDEFAKKESVKKIAGYLSDYYNSANH
IFSQEKKRKISIFRGIQAYNEIENVLKSKQIAPEYKNYFQYLKERITNQVQLLLTHQKSN
IEFKLLYKQLNFTENETDNFEVFQKIIDEK

Sequence of entity 2 (D, E, F), FASTA

>1LVC_2 calmodulin (chains D, E, F)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6
DOT	3'ANTHRANILOYL-2'-deoxy-adenosine-5'-triphosphate	C17 H21 N6 O13 P3	2
YB	Ytterbium (III) ion	Yb	3

Primary citation

Physiological calcium concentrations regulate calmodulin binding and catalysis of adenylyl cyclase exotoxins. Shen, Y., Lee, Y.-S., Soelaiman, S. et al. EMBO J (2002) 21:6721-6732. DOI 10.1093/emboj/cdf681 · PubMed

Other PDB entries of the same protein (UniProt P40136 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1K8T 2.6 Å, Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF)
1K90 2.75 Å, Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex…
1K93 2.95 Å, Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex…
1S26 3.0 Å, Structure of Anthrax Edema Factor-Calmodulin-alpha,beta-methyleneadenosine…
1SK6 3.2 Å, Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex…
1XFX 3.2 Å, Crystal structure of anthrax edema factor (EF) in complex with calmodulin in the…
6UZB 3.2 Å, Anthrax toxin protective antigen channels bound to edema factor
1XFZ 3.25 Å, Crystal structure of anthrax edema factor (EF) in complex with calmodulin in the…
1PK0 3.3 Å, Crystal Structure of the EF3-CaM complexed with PMEApp
1XFY 3.3 Å, Crystal structure of anthrax edema factor (EF) in complex with calmodulin
6VRA 3.3 Å, Anthrax octamer prechannel bound to full-length edema factor
1XFU 3.35 Å, Crystal structure of anthrax edema factor (EF) truncation mutant, EF-delta 64 in complex…

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