1XFZ: Anthrax edema factor

Crystal structure of anthrax edema factor (EF) in complex with calmodulin in the presence of 1 millimolar exogenously added calcium chloride. Determined by X-ray diffraction at 3.25 Å resolution. Released 3 May 2005.

Method: X-ray diffraction
Resolution: 3.25 Å
Organisms: Bacillus anthracis, Homo sapiens
Chains: 12
Atoms: 42,852
Mol. weight: 642.75 kDa
Ligands: CA, MG
Released: 3 May 2005

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

Secondary structure: helices and β-sheets

1XFZ contains 288 α-helices and 192 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.

Chain A: 40 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	1
α-helix	79-87	9
α-helix	91-99	9
β-strand	103-107	5	1
α-helix	137-139	3
β-strand	142-145	4	1
β-strand	151-155	5	1
α-helix	168-179	12
α-helix	180-182	3
α-helix	192-198	7
α-helix	230-233	4
α-helix	236-239	4
α-helix	243-249	7
α-helix	256-260	5
α-helix	262-270	9
α-helix	271-275	5
α-helix	276-282	7
α-helix	285-290	6
β-strand	297	1	2
α-helix	299-305	7
α-helix	309-318	10
α-helix	319-323	5
β-strand	324-328	5	2
α-helix	333-335	3
α-helix	336-341	6
β-strand	344-345	2	3
β-strand	365	1	4
α-helix	368-370	3
α-helix	381-393	13
β-strand	398-402	5	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	463	1	6
β-strand	467	1	6
β-strand	472-473	2	5
β-strand	475-480	6	4
β-strand	485-487	3	4
β-strand	488-489	2	3
β-strand	494-499	6	2
β-strand	500	1	7
α-helix	501-505	5
α-helix	510-517	8
α-helix	522-533	12
α-helix	534-538	5
β-strand	541	1	8
β-strand	549	1	8
α-helix	551-561	11
α-helix	580-582	3
β-strand	594-596	3	2
β-strand	602-604	3	2
α-helix	608-617	10
α-helix	620-622	3
β-strand	624	1	7
β-strand	636	1	9
β-strand	641	1	9
α-helix	648-651	4
α-helix	652-655	4
α-helix	657-659	3
α-helix	660-674	15
α-helix	685-704	20
α-helix	707-710	4
α-helix	714-736	23
α-helix	743-767	25
α-helix	773-778	6
α-helix	787-796	10

Chain B: 40 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	10
α-helix	76-87	12
α-helix	91-99	9
β-strand	103-107	5	10
α-helix	137-139	3
β-strand	142-145	4	10
β-strand	151-155	5	10
α-helix	168-179	12
α-helix	180-182	3
α-helix	192-198	7
α-helix	230-233	4
α-helix	236-239	4
α-helix	243-249	7
α-helix	256-260	5
α-helix	262-270	9
α-helix	271-275	5
α-helix	276-282	7
α-helix	285-290	6
β-strand	297	1	11
α-helix	299-305	7
α-helix	309-318	10
α-helix	319-323	5
β-strand	324-328	5	11
α-helix	333-335	3
α-helix	336-341	6
β-strand	344-345	2	12
β-strand	365	1	13
α-helix	368-370	3
α-helix	381-393	13
β-strand	398-402	5	13
α-helix	407-415	9
β-strand	420-427	8	14
β-strand	430-436	7	14
β-strand	442-446	5	14
β-strand	453-457	5	14
β-strand	463	1	15
β-strand	467	1	15
β-strand	472-473	2	14
β-strand	475-480	6	13
β-strand	485-487	3	13
β-strand	488-489	2	12
β-strand	494-499	6	11
β-strand	500	1	16
α-helix	501-505	5
α-helix	510-517	8
α-helix	522-533	12
α-helix	534-538	5
β-strand	541	1	17
β-strand	549	1	17
α-helix	551-561	11
α-helix	580-582	3
β-strand	594-596	3	11
β-strand	602-604	3	11
α-helix	608-617	10
α-helix	620-622	3
β-strand	624	1	16
β-strand	636	1	18
β-strand	641	1	18
α-helix	648-651	4
α-helix	652-655	4
α-helix	657-659	3
α-helix	660-674	15
α-helix	685-704	20
α-helix	707-710	4
α-helix	714-736	23
α-helix	743-765	23
α-helix	773-778	6
α-helix	787-796	10

Chain C: 40 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	19
α-helix	76-87	12
α-helix	91-99	9
β-strand	103-107	5	19
α-helix	137-139	3
β-strand	142-144	3	19
β-strand	151-155	5	19
α-helix	168-179	12
α-helix	180-182	3
α-helix	192-198	7
α-helix	230-233	4
α-helix	236-239	4
α-helix	243-249	7
α-helix	256-260	5
α-helix	262-270	9
α-helix	271-275	5
α-helix	276-282	7
α-helix	285-290	6
β-strand	297	1	20
α-helix	299-305	7
α-helix	309-318	10
α-helix	319-323	5
β-strand	324-328	5	20
α-helix	333-335	3
α-helix	336-341	6
β-strand	344-345	2	21
β-strand	365	1	22
α-helix	368-370	3
α-helix	381-393	13
β-strand	398-402	5	22
α-helix	407-415	9
β-strand	420-427	8	23
β-strand	430-436	7	23
β-strand	442-446	5	23
β-strand	453-457	5	23
β-strand	463	1	24
β-strand	467	1	24
β-strand	472-473	2	23
β-strand	475-480	6	22
β-strand	485-487	3	22
β-strand	488-489	2	21
β-strand	494-499	6	20
β-strand	500	1	25
α-helix	501-505	5
α-helix	510-517	8
α-helix	522-533	12
α-helix	534-538	5
β-strand	541	1	26
β-strand	549	1	26
α-helix	551-561	11
α-helix	580-582	3
β-strand	594-596	3	20
β-strand	602-604	3	20
α-helix	608-617	10
α-helix	620-622	3
β-strand	624	1	25
β-strand	636	1	27
β-strand	641	1	27
α-helix	648-651	4
α-helix	652-655	4
α-helix	657-659	3
α-helix	660-674	15
α-helix	685-704	20
α-helix	707-710	4
α-helix	714-736	23
α-helix	743-765	23
α-helix	773-778	6
α-helix	787-796	10

Chains D and F: 40 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	28
α-helix	79-87	9
α-helix	91-99	9
β-strand	103-107	5	28
α-helix	137-139	3
β-strand	142-145	4	28
β-strand	151-155	5	28
α-helix	168-179	12
α-helix	180-182	3
α-helix	192-198	7
α-helix	230-233	4
α-helix	236-239	4
α-helix	243-249	7
α-helix	256-260	5
α-helix	262-270	9
α-helix	271-275	5
α-helix	276-282	7
α-helix	285-290	6
β-strand	297	1	29
α-helix	299-305	7
α-helix	309-318	10
α-helix	319-323	5
β-strand	324-328	5	29
α-helix	333-335	3
α-helix	336-341	6
β-strand	344-345	2	30
β-strand	365	1	31
α-helix	368-370	3
α-helix	381-393	13
β-strand	398-402	5	31
α-helix	407-415	9
β-strand	420-427	8	32
β-strand	430-436	7	32
β-strand	442-446	5	32
β-strand	453-457	5	32
β-strand	463	1	33
β-strand	467	1	33
β-strand	472-473	2	32
β-strand	475-480	6	31
β-strand	485-487	3	31
β-strand	488-489	2	30
β-strand	494-499	6	29
β-strand	500	1	34
α-helix	501-505	5
α-helix	510-517	8
α-helix	522-533	12
α-helix	534-538	5
β-strand	541	1	35
β-strand	549	1	35
α-helix	551-561	11
α-helix	580-582	3
β-strand	594-596	3	29
β-strand	602-604	3	29
α-helix	608-617	10
α-helix	620-622	3
β-strand	624	1	34
β-strand	636	1	36
β-strand	641	1	36
α-helix	648-651	4
α-helix	652-655	4
α-helix	657-659	3
α-helix	660-674	15
α-helix	685-704	20
α-helix	707-710	4
α-helix	714-736	23
α-helix	743-765	23
α-helix	773-778	6
α-helix	787-796	10

Chain E: 40 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	37
α-helix	79-87	9
α-helix	91-99	9
β-strand	103-107	5	37
α-helix	137-139	3
β-strand	142-145	4	37
β-strand	151-155	5	37
α-helix	168-179	12
α-helix	180-182	3
α-helix	192-198	7
α-helix	230-233	4
α-helix	236-239	4
α-helix	243-249	7
α-helix	256-259	4
α-helix	262-270	9
α-helix	271-275	5
α-helix	276-282	7
α-helix	285-290	6
β-strand	297	1	38
α-helix	299-305	7
α-helix	309-318	10
α-helix	319-323	5
β-strand	324-328	5	38
α-helix	333-335	3
α-helix	336-341	6
β-strand	344-345	2	39
β-strand	365	1	40
α-helix	368-370	3
α-helix	381-393	13
β-strand	398-402	5	40
α-helix	407-415	9
β-strand	420-427	8	41
β-strand	430-436	7	41
β-strand	442-446	5	41
β-strand	453-457	5	41
β-strand	463	1	42
β-strand	467	1	42
β-strand	472-473	2	41
β-strand	475-480	6	40
β-strand	485-487	3	40
β-strand	488-489	2	39
β-strand	494-499	6	38
β-strand	500	1	43
α-helix	501-505	5
α-helix	510-517	8
α-helix	522-533	12
α-helix	534-538	5
β-strand	541	1	44
β-strand	549	1	44
α-helix	551-561	11
α-helix	580-582	3
β-strand	594-596	3	38
β-strand	602-604	3	38
α-helix	608-617	10
α-helix	620-622	3
β-strand	624	1	43
β-strand	636	1	45
β-strand	641	1	45
α-helix	648-651	4
α-helix	652-655	4
α-helix	657-659	3
α-helix	660-674	15
α-helix	685-704	20
α-helix	707-710	4
α-helix	714-736	23
α-helix	743-767	25
α-helix	773-778	6
α-helix	787-796	10

Chains O and Q: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
β-strand	26-27	2	55
α-helix	29-38	10
α-helix	47-52	6
β-strand	63-64	2	55
α-helix	65-71	7
α-helix	82-92	11
β-strand	99-100	2	56
α-helix	102-111	10
α-helix	118-128	11
β-strand	136-137	2	56
α-helix	138-146	9

Chain P: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
β-strand	27-28	2	57
α-helix	29-38	10
α-helix	47-52	6
β-strand	62-63	2	57
α-helix	65-71	7
α-helix	82-92	11
β-strand	99-100	2	58
α-helix	102-111	10
α-helix	118-128	11
β-strand	136-137	2	58
α-helix	138-146	9

Chains R, S and T: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
β-strand	26-28	3	61
α-helix	29-38	10
α-helix	47-52	6
β-strand	62-64	3	61
α-helix	65-71	7
α-helix	82-92	11
β-strand	99-100	2	62
α-helix	102-111	10
α-helix	118-128	11
β-strand	136-137	2	62
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 2	O, P, Q, R, S, T	protein	149	Homo sapiens	P0DP23 (AlphaFold model)

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

>1XFZ_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 (O, P, Q, R, S, T), FASTA

>1XFZ_2 Calmodulin 2 (chains O, P, Q, R, S, T)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDQMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	18
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
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…
1XFV 3.35 Å, Crystal structure of anthrax edema factor (EF) in complex with calmodulin and 3' deoxy-ATP

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