1Y0V: Anthrax edema factor

Crystal structure of anthrax edema factor (EF) in complex with calmodulin and pyrophosphate. Determined by X-ray diffraction at 3.6 Å resolution. Released 3 May 2005.

Method: X-ray diffraction
Resolution: 3.6 Å
Organisms: Bacillus anthracis, Xenopus laevis
Chains: 12
Atoms: 42,906
Mol. weight: 641.31 kDa
Ligands: CA, POP, MG
Released: 3 May 2005

Explore 1Y0V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Y0V contains 257 α-helices and 178 β-strands across 12 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.

Chains A, B and E: 35 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	1
α-helix	79-86	8
α-helix	91-97	7
β-strand	103-107	5	1
α-helix	137-139	3
β-strand	143-144	2	1
β-strand	151-155	5	1
α-helix	170-176	7
α-helix	180-182	3
α-helix	192-195	4
α-helix	236-248	13
α-helix	256-259	4
α-helix	264-270	7
α-helix	271-275	5
α-helix	276-290	15
α-helix	298-300	3
α-helix	309-322	14
β-strand	324-328	5	2
α-helix	333-341	9
α-helix	343-344	2
β-strand	345	1	3
β-strand	365	1	4
α-helix	368-370	3
α-helix	381-393	13
β-strand	399-402	4	4
α-helix	407-415	9
β-strand	420-427	8	5
β-strand	430-436	7	5
β-strand	442-446	5	5
β-strand	453-457	5	5
β-strand	472-473	2	5
β-strand	475-480	6	4
β-strand	485-487	3	4
α-helix	488	1
β-strand	489	1	3
β-strand	494-499	6	2
β-strand	500	1	6
α-helix	501-507	7
α-helix	510-517	8
α-helix	524-535	12
β-strand	541-542	2	7
β-strand	548-549	2	7
α-helix	552-564	13
α-helix	580-582	3
β-strand	594-596	3	2
β-strand	602-604	3	2
α-helix	608-618	11
α-helix	620-622	3
β-strand	624	1	6
β-strand	635-636	2	8
β-strand	641-642	2	8
α-helix	648-651	4
α-helix	657-659	3
α-helix	660-671	12
α-helix	687-704	18
α-helix	707-711	5
α-helix	715-735	21
α-helix	743-764	22
α-helix	773-778	6
α-helix	787-796	10

Chains C and F: 35 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	17
α-helix	79-86	8
α-helix	91-97	7
β-strand	103-107	5	17
α-helix	137-139	3
β-strand	143-144	2	17
β-strand	151-155	5	17
α-helix	170-176	7
α-helix	180-182	3
α-helix	192-195	4
α-helix	236-248	13
α-helix	256-259	4
α-helix	264-270	7
α-helix	271-275	5
α-helix	276-290	15
α-helix	298-300	3
α-helix	309-322	14
β-strand	324-328	5	18
α-helix	333-341	9
α-helix	343-344	2
β-strand	345	1	19
β-strand	365	1	20
α-helix	368-370	3
α-helix	381-393	13
β-strand	399-402	4	20
β-strand	404	1	21
α-helix	407-415	9
β-strand	420-427	8	22
β-strand	430-436	7	22
β-strand	442-446	5	22
β-strand	452	1	21
β-strand	453-457	5	22
β-strand	472-473	2	22
β-strand	475-480	6	20
β-strand	485-487	3	20
α-helix	488	1
β-strand	489	1	19
β-strand	494-499	6	18
β-strand	500	1	23
α-helix	501-507	7
α-helix	510-517	8
α-helix	524-535	12
β-strand	541-542	2	24
β-strand	548-549	2	24
α-helix	552-564	13
α-helix	580-582	3
β-strand	594-596	3	18
β-strand	602-604	3	18
α-helix	608-618	11
α-helix	620-622	3
β-strand	624	1	23
β-strand	635-636	2	25
β-strand	641-642	2	25
α-helix	648-651	4
α-helix	657-659	3
α-helix	660-671	12
α-helix	687-704	18
α-helix	707-711	5
α-helix	715-735	21
α-helix	743-764	22
α-helix	773-778	6
α-helix	787-796	10

Chain D: 34 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	26
α-helix	79-86	8
α-helix	91-97	7
β-strand	103-107	5	26
α-helix	137-139	3
β-strand	143-144	2	26
β-strand	151-155	5	26
α-helix	170-176	7
α-helix	180-182	3
α-helix	192-195	4
α-helix	236-248	13
α-helix	256-259	4
α-helix	264-270	7
α-helix	271-275	5
α-helix	276-290	15
α-helix	298-300	3
α-helix	309-322	14
β-strand	324-328	5	27
α-helix	333-341	9
β-strand	345	1	28
β-strand	365	1	29
α-helix	368-370	3
α-helix	381-393	13
β-strand	399-402	4	29
α-helix	407-415	9
β-strand	420-427	8	30
β-strand	430-436	7	30
β-strand	442-446	5	30
β-strand	453-457	5	30
β-strand	472-473	2	30
β-strand	475-480	6	29
β-strand	485-487	3	29
α-helix	488	1
β-strand	489	1	28
β-strand	494-499	6	27
β-strand	500	1	31
α-helix	501-507	7
α-helix	510-517	8
α-helix	524-535	12
β-strand	541-542	2	32
β-strand	548-549	2	32
α-helix	552-564	13
α-helix	580-582	3
β-strand	594-596	3	27
β-strand	602-604	3	27
α-helix	608-618	11
α-helix	620-622	3
β-strand	624	1	31
β-strand	635-636	2	33
β-strand	641-642	2	33
α-helix	648-651	4
α-helix	657-659	3
α-helix	660-671	12
α-helix	687-704	18
α-helix	707-711	5
α-helix	715-735	21
α-helix	743-764	22
α-helix	773-778	6
α-helix	787-796	10

Chains H, I, J, K, L and M: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-18	12
β-strand	26-27	2	51
α-helix	29-38	10
β-strand	63-64	2	51
α-helix	65-68	4
α-helix	69-71	3
α-helix	82-90	9
β-strand	99	1	52
α-helix	102-111	10
α-helix	124-128	5
β-strand	137	1	52
α-helix	138-146	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calmodulin-sensitive adenylate cyclase	A, B, C, D, E, F	protein	777	Bacillus anthracis	P40136 (AlphaFold model)
Calmodulin	H, I, J, K, L, M	protein	146	Xenopus laevis	P0DP33 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>1Y0V_1 Calmodulin-sensitive adenylate cyclase (chains A, B, C, D, E, F)
MHHHHHHAAAMNEHYTESDIKRNHKTEKNKTEKEKFKDSINNLVKTEFTNETLDKIQQTQ
DLLKKIPKDVLEIYSELGGEIYFTDIDLVEHKELQDLSEEEKNSMNSRGEKVPFASRFVF
EKKRETPKLIINIKDYAINSEQSKEVYYEIGKGISLDIISKDKSLDPEFLNLIKSLSDDS
DSSDLLFSQKFKEKLELNNKSIDINFIKENLTEFQHAFSLAFSYYFAPDHRTVLELYAPD
MFEYMNKLEKGGFEKISESLKKEGVEKDRIDVLKGEKALKASGLVPEHADAFKKIARELN
TYILFRPVNKLATNLIKSGVATKGLNVHGKSSDWGPVAGYIPFDQDLSKKHGQQLAVEKG
NLENKKSITEHEGEIGKIPLKLDHLRIEELKENGIILKGKKEIDNGKKYYLLESNNQVYE
FRISDENNEVQYKTKEGKITVLGEKFNWRNIEVMAKNVEGVLKPLTADYDLFALAPSLTE
IKKQIPQKEWDKVVNTPNSLEKQKGVTNLLIKYGIERKPDSTKGTLSNWQKQMLDRLNEA
VKYTGYTGGDVVNHGTEQDNEEFPEKDNEIFIINPEGEFILTKNWEMTGRFIEKNITGKD
YLYYFNRSYNKIAPGNKAYIEWTDPITKAKINTIPTSAEFIKNLSSIRRSSNVGVYKDSG
DKDEFAKKESVKKIAGYLSDYYNSANHIFSQEKKRKISIFRGIQAYNEIENVLKSKQIAP
EYKNYFQYLKERITNQVQLLLTHQKSNIEFKLLYKQLNFTENETDNFEVFQKIIDEK

Sequence of entity 2 (H, I, J, K, L, M), FASTA

>1Y0V_2 Calmodulin (chains H, I, J, K, L, M)
AATEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGT
IDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVD
EMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	18
POP	Pyrophosphate 2-	H2 O7 P2	6
MG	Magnesium ion	Mg	6

Primary citation

Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor. Shen, Y., Zhukovskaya, N.L., Guo, Q. et al. EMBO J (2005) 24:929-941. DOI 10.1038/sj.emboj.7600574 · 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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