1XFV: Anthrax edema factor

Crystal structure of anthrax edema factor (EF) in complex with calmodulin and 3' deoxy-ATP. Determined by X-ray diffraction at 3.35 Å resolution. Released 3 May 2005.

Method: X-ray diffraction
Resolution: 3.35 Å
Organisms: Bacillus anthracis, Homo sapiens
Chains: 12
Atoms: 43,044
Mol. weight: 645.84 kDa
Ligands: CA, 3AT, MG
Released: 3 May 2005

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

Secondary structure: helices and β-sheets

1XFV contains 272 α-helices and 204 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, E and F: 37 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	1
α-helix	79-86	8
α-helix	91-99	9
β-strand	103-106	4	1
β-strand	130	1	2
β-strand	132	1	2
α-helix	137-139	3
β-strand	142-144	3	1
β-strand	151-154	4	1
α-helix	165-167	3
α-helix	168-176	9
α-helix	192-199	8
α-helix	241-249	9
α-helix	255-259	5
α-helix	262-270	9
α-helix	271-275	5
α-helix	276-279	4
α-helix	285-288	4
β-strand	296-297	2	3
α-helix	298-300	3
α-helix	301-305	5
α-helix	309-322	14
β-strand	324-328	5	3
α-helix	330-332	3
α-helix	333-341	9
β-strand	344-345	2	4
β-strand	365	1	5
α-helix	368-370	3
α-helix	377-380	4
α-helix	383-393	11
β-strand	398-402	5	5
α-helix	407-415	9
β-strand	420	1	6
β-strand	424-426	3	7
β-strand	431-433	3	7
β-strand	436	1	6
β-strand	442-447	6	7
β-strand	453-457	5	7
β-strand	472-473	2	7
β-strand	475-481	7	5
β-strand	484-487	4	5
β-strand	488-489	2	4
β-strand	494-499	6	3
β-strand	500	1	8
α-helix	501-505	5
α-helix	514-517	4
α-helix	522-533	12
α-helix	534-538	5
β-strand	541	1	9
β-strand	549	1	9
α-helix	551-566	16
α-helix	580-582	3
β-strand	593-596	4	3
β-strand	603-605	3	3
α-helix	608-615	8
α-helix	616-620	5
β-strand	624	1	8
β-strand	635-636	2	10
β-strand	641-642	2	10
α-helix	649-655	7
α-helix	660-671	12
α-helix	687-704	18
α-helix	707-711	5
α-helix	714-735	22
α-helix	743-762	20
α-helix	773-778	6
α-helix	787-795	9

Chain B: 37 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	11
α-helix	79-86	8
α-helix	91-99	9
β-strand	103-106	4	11
β-strand	130	1	12
β-strand	132	1	12
α-helix	137-139	3
β-strand	142-144	3	11
β-strand	151-154	4	11
α-helix	165-167	3
α-helix	168-176	9
α-helix	192-199	8
α-helix	241-249	9
α-helix	255-259	5
α-helix	262-270	9
α-helix	271-275	5
α-helix	276-279	4
α-helix	285-288	4
β-strand	296-297	2	13
α-helix	298-300	3
α-helix	301-305	5
α-helix	309-322	14
β-strand	324-328	5	13
α-helix	330-332	3
α-helix	333-341	9
β-strand	344-345	2	14
β-strand	365	1	15
α-helix	368-370	3
α-helix	377-380	4
α-helix	383-393	11
β-strand	398-402	5	15
α-helix	407-415	9
β-strand	420	1	16
β-strand	424-426	3	17
β-strand	431-433	3	17
β-strand	436	1	16
β-strand	442-447	6	17
β-strand	453-457	5	17
β-strand	472-473	2	17
β-strand	475-481	7	15
β-strand	484-487	4	15
β-strand	488-489	2	14
β-strand	494-499	6	13
β-strand	500	1	18
α-helix	501-505	5
α-helix	514-517	4
α-helix	522-533	12
α-helix	534-538	5
β-strand	541	1	19
β-strand	549	1	19
α-helix	551-566	16
α-helix	580-582	3
β-strand	593-596	4	13
β-strand	603-605	3	13
α-helix	608-614	7
α-helix	615-620	6
β-strand	624	1	18
β-strand	635-636	2	20
β-strand	641-642	2	20
α-helix	649-655	7
α-helix	660-671	12
α-helix	687-704	18
α-helix	707-711	5
α-helix	714-735	22
α-helix	743-762	20
α-helix	773-778	6
α-helix	787-795	9

Chain C: 37 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	21
α-helix	79-86	8
α-helix	91-99	9
β-strand	103-106	4	21
β-strand	130	1	22
β-strand	132	1	22
α-helix	137-139	3
β-strand	142-144	3	21
β-strand	151-154	4	21
α-helix	165-167	3
α-helix	168-176	9
α-helix	192-199	8
α-helix	241-249	9
α-helix	255-259	5
α-helix	262-270	9
α-helix	271-275	5
α-helix	276-279	4
α-helix	285-288	4
β-strand	296-297	2	23
α-helix	298-300	3
α-helix	301-305	5
α-helix	309-322	14
β-strand	324-328	5	23
α-helix	330-332	3
α-helix	333-341	9
β-strand	344-345	2	24
β-strand	365	1	25
α-helix	368-370	3
α-helix	377-380	4
α-helix	383-393	11
β-strand	398-402	5	25
α-helix	407-415	9
β-strand	420	1	26
β-strand	424-426	3	27
β-strand	431-433	3	27
β-strand	436	1	26
β-strand	442-447	6	27
β-strand	453-457	5	27
β-strand	472-473	2	27
β-strand	475-481	7	25
β-strand	484-487	4	25
β-strand	488-489	2	24
β-strand	494-499	6	23
β-strand	500	1	28
α-helix	501-505	5
α-helix	514-517	4
α-helix	522-533	12
α-helix	534-538	5
β-strand	541	1	29
β-strand	549	1	29
α-helix	551-566	16
α-helix	580-582	3
β-strand	593-596	4	23
β-strand	603-605	3	23
α-helix	608-615	8
α-helix	616-620	5
β-strand	624	1	28
β-strand	635-636	2	30
β-strand	641-642	2	30
α-helix	649-655	7
α-helix	660-671	12
α-helix	687-704	18
α-helix	707-711	5
α-helix	714-735	22
α-helix	743-765	23
α-helix	773-778	6
α-helix	787-795	9

Chain D: 38 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	31
α-helix	79-86	8
α-helix	91-99	9
β-strand	103-106	4	31
β-strand	130	1	32
β-strand	132	1	32
α-helix	137-139	3
β-strand	142-144	3	31
β-strand	151-154	4	31
α-helix	165-167	3
α-helix	168-176	9
α-helix	192-199	8
α-helix	235-237	3
α-helix	241-249	9
α-helix	255-259	5
α-helix	262-270	9
α-helix	271-275	5
α-helix	276-279	4
α-helix	285-288	4
β-strand	296-297	2	33
α-helix	298-300	3
α-helix	301-305	5
α-helix	309-322	14
β-strand	324-328	5	33
α-helix	330-332	3
α-helix	333-341	9
β-strand	344-345	2	34
β-strand	365	1	35
α-helix	368-370	3
α-helix	377-380	4
α-helix	383-393	11
β-strand	398-402	5	35
α-helix	407-415	9
β-strand	420	1	36
β-strand	424-426	3	37
β-strand	431-433	3	37
β-strand	436	1	36
β-strand	442-447	6	37
β-strand	453-457	5	37
β-strand	472-473	2	37
β-strand	475-481	7	35
β-strand	484-487	4	35
β-strand	488-489	2	34
β-strand	494-499	6	33
β-strand	500	1	38
α-helix	501-505	5
α-helix	514-517	4
α-helix	522-533	12
α-helix	534-538	5
β-strand	541	1	39
β-strand	549	1	39
α-helix	551-566	16
α-helix	580-582	3
β-strand	593-596	4	33
β-strand	603-605	3	33
α-helix	608-615	8
α-helix	616-620	5
β-strand	624	1	38
β-strand	635-636	2	40
β-strand	641-642	2	40
α-helix	649-655	7
α-helix	660-671	12
α-helix	687-704	18
α-helix	707-711	5
α-helix	714-735	22
α-helix	743-762	20
α-helix	773-778	6
α-helix	787-795	9

Chains O, Q and R: 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	53-55	3
β-strand	62-64	3	61
α-helix	68-71	4
α-helix	81-92	12
β-strand	99-100	2	62
α-helix	102-109	8
α-helix	118-128	11
β-strand	136-137	2	62
α-helix	138-146	9

Chains P and S: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
β-strand	26-28	3	63
α-helix	29-38	10
α-helix	50-53	4
β-strand	62-64	3	63
α-helix	68-71	4
α-helix	81-92	12
β-strand	99-100	2	64
α-helix	102-109	8
α-helix	118-128	11
β-strand	136-137	2	64
α-helix	138-146	9

Chain T: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
α-helix	17-19	3
β-strand	26-28	3	71
α-helix	29-38	10
α-helix	53-55	3
β-strand	62-64	3	71
α-helix	68-71	4
α-helix	81-92	12
β-strand	99-100	2	72
α-helix	102-109	8
α-helix	118-128	11
β-strand	136-137	2	72
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

>1XFV_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

>1XFV_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
3AT	3'-deoxyadenosine-5'-triphosphate	C10 H16 N5 O12 P3	6
MG	Magnesium ion	Mg	12

Primary citation

Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor. Shen, Q., 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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