6VRA: Anthrax octamer prechannel

Anthrax octamer prechannel bound to full-length edema factor. Determined by electron microscopy at 3.3 Å resolution. Released 16 Dec 2020.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Bacillus anthracis
Chains: 12
Atoms: 57,744
Mol. weight: 1017.07 kDa
Ligands: CA
Released: 16 Dec 2020

Explore 6VRA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VRA contains 288 α-helices and 412 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, C, E and G: 16 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	185-190	6
β-strand	192-196	5	1
β-strand	201-205	5	1
α-helix	208-211	4
β-strand	219	1	1
α-helix	235-240	6
α-helix	249-252	4
β-strand	256	1	2
β-strand	262-273	12	3
β-strand	288-292	5	3
β-strand	295-297	3	4
β-strand	328-333	6	4
α-helix	346-350	5
β-strand	357-368	12	3
β-strand	374	1	5
β-strand	382-385	4	4
β-strand	389-393	5	4
α-helix	396-397	2
β-strand	405	1	5
β-strand	409-410	2	3
α-helix	417-418	2
β-strand	419-420	2	3
β-strand	433-435	3	3
α-helix	436-445	10
β-strand	447-452	6	4
β-strand	459-462	4	6
β-strand	469-472	4	6
α-helix	477-486	10
β-strand	488-493	6	2
β-strand	501-506	6	2
β-strand	508	1	7
α-helix	519-520	2
β-strand	522	1	8
α-helix	523-530	8
β-strand	534	1	9
β-strand	541-542	2	9
β-strand	545-546	2	9
α-helix	547-549	3
β-strand	550-554	5	2
α-helix	556-568	13
β-strand	582	1	8
β-strand	584	1	7
β-strand	588-593	6	2
β-strand	596-598	3	10
β-strand	604-607	4	10
α-helix	609-615	7
β-strand	619-622	4	11
β-strand	626-629	4	11
α-helix	635-637	3
β-strand	639-647	9	12
β-strand	654-655	2	12
β-strand	666-668	3	11
β-strand	674-677	4	11
α-helix	679-681	3
β-strand	695-702	8	12
β-strand	724-730	7	12

Chains B, D, F and H: 17 helices, 43 β-strands

Element	Residues	Length	Sheet
α-helix	185-190	6
β-strand	192-196	5	13
β-strand	201-205	5	13
α-helix	208-211	4
β-strand	219	1	13
α-helix	235-240	6
α-helix	249-252	4
β-strand	256	1	14
β-strand	262-273	12	15
β-strand	289-292	4	15
β-strand	296-297	2	16
β-strand	328-331	4	16
α-helix	346-350	5
β-strand	358-368	11	15
β-strand	374	1	17
β-strand	381-385	5	16
β-strand	389-394	6	16
α-helix	396-397	2
β-strand	405	1	17
β-strand	409-410	2	15
β-strand	419-420	2	15
β-strand	425	1	18
β-strand	428	1	18
β-strand	432-434	3	15
α-helix	436-445	10
β-strand	448-452	5	16
β-strand	459-463	5	19
β-strand	468-472	5	19
α-helix	477-479	3
α-helix	481-486	6
β-strand	489-493	5	14
β-strand	501-505	5	14
β-strand	508	1	20
α-helix	514-516	3
α-helix	519-520	2
β-strand	522	1	21
α-helix	523-530	8
β-strand	534	1	22
β-strand	541-542	2	22
β-strand	545-546	2	22
α-helix	547-549	3
β-strand	550-554	5	14
α-helix	556-568	13
β-strand	582	1	21
β-strand	584	1	20
β-strand	588-593	6	14
β-strand	596-598	3	23
β-strand	604-607	4	23
α-helix	609-615	7
β-strand	619-622	4	24
β-strand	626-629	4	24
α-helix	635-637	3
β-strand	639-647	9	25
β-strand	655	1	25
β-strand	667-669	3	24
β-strand	673-677	5	24
α-helix	679-681	3
β-strand	695-702	8	25
β-strand	724-727	4	25
β-strand	730	1	25

Chains I, J, K and L: 39 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	22-27	6
β-strand	34	1	13
α-helix	42-53	12
α-helix	58-67	10
β-strand	71-74	4	101
α-helix	104-106	3
β-strand	109-112	4	101
β-strand	118-122	5	101
α-helix	132-143	12
α-helix	158-167	10
α-helix	179-188	10
α-helix	194-199	6
α-helix	201-216	16
α-helix	222-227	6
α-helix	229-237	9
α-helix	238-242	5
α-helix	243-254	12
α-helix	266-272	7
α-helix	276-289	14
β-strand	294-296	3	102
α-helix	300-308	9
β-strand	312	1	103
α-helix	320	1
β-strand	321	1	104
α-helix	322	1
β-strand	330	1	103
α-helix	331-332	2
α-helix	335-337	3
β-strand	338	1	104
α-helix	347-360	14
α-helix	375-379	5
α-helix	381-383	3
α-helix	394-396	3
α-helix	439-441	3
β-strand	445	1	105
β-strand	448	1	106
β-strand	451	1	106
β-strand	454	1	105
β-strand	456	1	103
α-helix	457-459	3
β-strand	460-461	2	102
β-strand	463-464	2	107
α-helix	468-474	7
α-helix	478-484	7
α-helix	489-504	16
α-helix	518-528	11
α-helix	529-531	3
β-strand	561-563	3	102
β-strand	569-571	3	102
α-helix	575-581	7
α-helix	582-586	5
β-strand	594-595	2	107
α-helix	627-638	12
α-helix	652-670	19
α-helix	681-702	22
α-helix	710-734	25
β-strand	738	1	101
α-helix	740-746	7
α-helix	756-764	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protective antigen	A, C, E, G	protein	735	Bacillus anthracis	P13423 (AlphaFold model)
Protective antigen	B, D, F, H	protein	735	Bacillus anthracis	P13423 (AlphaFold model)
Calmodulin-sensitive adenylate cyclase	I, J, K, L	protein	767	Bacillus anthracis	P40136 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>6VRA_1 Protective antigen (chains A, C, E, G)
QENRLLNESESSSQGLLGYYFSDLNFQAPMVVTSSTTGDLSIPSSELENIPSENQYFQSA
IWSGFIKVKKSDEYTFATSADNHVTMWVDDQEVINKASNSNKIRLEKGRLYQIKIQYQRE
DPTEKGLDFKLYWTDSQNKKEVISSDNLQLPELKQKSSNSLEVLFQGSTSAGPTVPDRDN
DGIPDSLEVEGYTVDVKNKRTFLSPWISNIHEKKGLTKYKSSPEKWSTASDPYSDFEKVT
GRIDGNVSPEANHPLVAAYPIVHVDMENIILSKNEDQSTQNTDSQTRTISKNTSTSRTHT
SEVHGNAEVHASFFDIGGSVSAGFSNSNSSTVAIDHSLSLAGERTWAETMGLNTADTARL
NANIRYVNTGTAPIYNVLPTTSLVLGKNQTLATIKAKENQLSQILAPNNYYPSKNLAPIA
LNAQDDFSSTPITMNYNQFLELEKTKQLRLDTDQVYGNIATYNFENGRVRVDTGSNWSEV
LPQIQETTARIIFNGKDLNLVERRIAAVNPSDPLETTKPDMTLKEALKIAFGFNEPNGNL
QYQGKDITEFDFNFDQQTSQNIKNQLAELNATNIYTVLDKIKLNAKMNILIRDKRFHYDR
NNIAVGADESVVKEAHREVINSSTEGLLLNIDKDIRKILSGYIVEIEDTEGLKEVINDRY
DMLNISSLRQDGKTFIDFKKYNDKLPLYISNPNYKVNVYAVTKENTIINPSENGDTSTNG
IKKILIFSKKGYEIG

Sequence of entity 2 (B, D, F, H), FASTA

>6VRA_2 Protective antigen (chains B, D, F, H)
QENRLLNESESSSQGLLGYYFSDLNFQAPMVVTSSTTGDLSIPSSELENIPSENQYFQSA
IWSGFIKVKKSDEYTFATSADNHVTMWVDDQEVINKASNSNKIRLEKGRLYQIKIQYQRE
NPTEKGLDFKLYWTDSQNKKEVISSDNLQLPELKQKSSNSLEVLFQGSTSAGPTVPDRDN
DGIPDSLEVEGYTVDVKNKRTFLSPWISNIHEKKGLTKYKSSPEKWSTASDPYSDFEKVT
GRIDKNVSPEARHPLVAAYPIVHVDMENIILSKNEDQSTQNTDSQTRTISKNTSTSRTHT
SEVHGNAEVHASFFDIGGSVSAGFSNSNSSTVAIDHSLSLAGERTWAETMGLNTADTARL
NANIRYVNTGTAPIYNVLPTTSLVLGKNQTLATIKAKENQLSQILAPNNYYPSKNLAPIA
LNAQDDFSSTPITMNYNQFLELEKTKQLRLDTDQVYGNIATYNFENGRVRVDTGSNWSEV
LPQIQETTARIIFNGKDLNLVERRIAAVNPSKPLETTKPDMTLKEALKIAFGFNEPNGNL
QYQGKDITEFDFNFDQQTSQNIKNQLAELNATNIYTVLDKIKLNAKMNILIRDKRFHYDR
NNIAVGADESVVKEAHREVINSSTEGLLLNIDKDIRKILSGYIVEIEDTEGLKEVINDRY
DMLNISSLRQDGKTFIDFKKYNDKLPLYISNPNYKVNVYAVTKENTIINPSENGDTSTNG
IKKILIFSKKGYEIG

Sequence of entity 3 (I, J, K, L), FASTA

>6VRA_3 Calmodulin-sensitive adenylate cyclase (chains I, J, K, L)
MNEHYTESDIKRNHKTEKNKTEKEKFKDSINNLVKTEFTNETLDKIQQTQDLLKKIPKDV
LEIYSELGGEIYFTDIDLVEHKELQDLSEEEKNSMNSRGEKVPFASRFVFEKKRETPKLI
INIKDYAINSEQSKEVYYEIGKGISLDIISKDKSLDPEFLNLIKSLSDDSDSSDLLFSQK
FKEKLELNNKSIDINFIKENLTEFQHAFSLAFSYYFAPDHRTVLELYAPDMFEYMNKLEK
GGFEKISESLKKEGVEKDRIDVLKGEKALKASGLVPEHADAFKKIARELNTYILFRPVNK
LATNLIKSGVATKGLNVHGKSSDWGPVAGYIPFDQDLSKKHGQQLAVEKGNLENKKSITE
HEGEIGKIPLKLDHLRIEELKENGIILKGKKEIDNGKKYYLLESNNQVYEFRISDENNEV
QYKTKEGKITVLGEKFNWRNIEVMAKNVEGVLKPLTADYDLFALAPSLTEIKKQIPQKEW
DKVVNTPNSLEKQKGVTNLLIKYGIERKPDSTKGTLSNWQKQMLDRLNEAVKYTGYTGGD
VVNHGTEQDNEEFPEKDNEIFIINPEGEFILTKNWEMTGRFIEKNITGKDYLYYFNRSYN
KIAPGNKAYIEWTDPITKAKINTIPTSAEFIKNLSSIRRSSNVGVYKDSGDKDEFAKKES
VKKIAGYLSDYYNSANHIFSQEKKRKISIFRGIQAYNEIENVLKSKQIAPEYKNYFQYLK
ERITNQVQLLLTHQKSNIEFKLLYKQLNFTENETDNFEVFQKIIDEK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	16

Primary citation

Atomic Structures of Anthrax Prechannel Bound with Full-Length Lethal and Edema Factors. Zhou, K., Liu, S., Hardenbrook, N.J. et al. Structure (2020) 28:879-887.e3. DOI 10.1016/j.str.2020.05.009 · PubMed

Other PDB entries of the same protein (UniProt P13423 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3TEW 1.45 Å, Crystal Structure of Anthrax Protective Antigen (Membrane Insertion Loop Deleted) to…
4H2A 1.62 Å, Crystal structure of wild type protective antigen to 1.62 A (pH 7.5)
3MHZ 1.7 Å, 1.7A structure of 2-fluorohistidine labeled Protective Antigen
3TEX 1.7 Å, Crystal Structure of Anthrax Protective Antigen (Membrane Insertion Loop Deleted) to…
4NAM 1.7 Å, 1.7A structure of 5-Fluoro Tryptophan Labeled Protective Antigen (W206Y)
3TEZ 1.83 Å, Crystal Structure of Anthrax Protective Antigen Mutant S337C N664C and dithiolacetone…
4EE2 1.91 Å, Crystal Structure of Anthrax Protective Antigen K446M Mutant to 1.91-A Resolution
5FR3 1.94 Å, X-ray crystal structure of aggregation-resistant protective antigen of Bacillus…
3INO 1.95 Å, 1.95A Resolution Structure of Protective Antigen Domain 4
3Q8B 2.0 Å, Crystal structure of WT Protective Antigen (pH 9.0)
3Q8E 2.1 Å, Crystal structure of Protective Antigen W346F (pH 8.5)
1ACC 2.1 Å, Anthrax protective antigen

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