8BR0: Actin, alpha skeletal muscle, intermediate form

Name: PDB 8BR0: ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin (residue Q3455 to L3863) in complex with 3'deoxyCTP and two manganese cations bound to Latrunculin-B-ADP-Mn-actin
Published: 2023-09-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin (residue Q3455 to L3863) in complex with 3'deoxyCTP and two manganese cations bound to Latrunculin-B-ADP-Mn-actin. Determined by X-ray diffraction at 2.22 Å resolution. Released 20 Sept 2023.

Method: X-ray diffraction
Resolution: 2.22 Å
Organisms: Oryctolagus cuniculus, Vibrio nigripulchritudo SFn135
Chains: 4
Atoms: 12,638
Mol. weight: 217.1 kDa
Ligands: CH1, MN, ADP, LAB
Released: 20 Sept 2023

Explore 8BR0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BR0 contains 110 α-helices and 87 β-strands across 4 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: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-37	3	2
β-strand	53-54	2	2
α-helix	56-60	5
α-helix	62-64	3
β-strand	66-68	3	2
β-strand	71-72	2	3
β-strand	75-76	2	3
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	1
α-helix	137-144	8
β-strand	150-155	6	4
β-strand	160-166	7	4
β-strand	169-170	2	4
α-helix	172-174	3
β-strand	176-178	3	4
α-helix	182-193	12
α-helix	194-196	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	5
β-strand	247-250	4	5
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	287-294	8
β-strand	297-300	4	4
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	4
α-helix	338-347	10
α-helix	350-352	3
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	367-370	4

Chain B: 32 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	468-470	3	6
β-strand	473-475	3	6
α-helix	476-478	3
α-helix	481-483	3
α-helix	490-503	14
β-strand	505-509	5	7
α-helix	514-516	3
α-helix	517-521	5
β-strand	527	1	8
α-helix	535-536	2
β-strand	537	1	9
β-strand	543	1	9
β-strand	545	1	8
β-strand	547	1	10
α-helix	550-552	3
α-helix	555-558	4
α-helix	561-573	13
β-strand	578-581	4	10
β-strand	583-584	2	11
α-helix	586-590	5
α-helix	591-595	5
α-helix	600-602	3
β-strand	603-604	2	11
α-helix	605	1
β-strand	611-616	6	11
β-strand	621-631	11	11
β-strand	634-643	10	11
β-strand	646-649	4	11
β-strand	651-654	4	10
α-helix	660	1
β-strand	661	1	10
α-helix	662	1
β-strand	663	1	8
α-helix	666-667	2
β-strand	668-674	7	7
α-helix	675-677	3
α-helix	680-682	3
β-strand	685	1	12
α-helix	690-696	7
α-helix	699-701	3
α-helix	704-711	8
α-helix	713-719	7
α-helix	721-723	3
β-strand	727	1	12
α-helix	729-741	13
α-helix	756-758	3
α-helix	764-767	4
β-strand	770-773	4	7
α-helix	776-779	4
α-helix	791-794	4
β-strand	796-797	2	7
β-strand	803-805	3	7
α-helix	808-820	13
β-strand	823-824	2	7
α-helix	825	1
α-helix	829-832	4
α-helix	848-861	14

Chain C: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	13
β-strand	16-21	6	13
β-strand	29-32	4	13
β-strand	35-38	4	14
β-strand	53-54	2	14
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	14
β-strand	71-72	2	15
β-strand	75-76	2	15
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	13
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	13
α-helix	137-143	7
β-strand	150-155	6	16
β-strand	160-166	7	16
β-strand	169-170	2	16
α-helix	172-174	3
β-strand	176-178	3	16
α-helix	182-193	12
α-helix	194-196	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	17
β-strand	247-250	4	17
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	287-294	8
β-strand	297-300	4	16
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	16
α-helix	338-347	10
β-strand	357-358	2	13
α-helix	359-365	7
α-helix	367-370	4

Chain D: 31 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	466-467	2
β-strand	468-470	3	18
β-strand	473-475	3	18
α-helix	481-483	3
α-helix	490-503	14
β-strand	505-509	5	19
α-helix	514-516	3
α-helix	517-521	5
β-strand	527	1	20
α-helix	535-536	2
β-strand	537	1	21
β-strand	543	1	21
β-strand	547	1	22
α-helix	550-552	3
α-helix	555-558	4
α-helix	561-573	13
β-strand	578-581	4	22
β-strand	583-584	2	23
α-helix	586-590	5
α-helix	591-595	5
α-helix	600-602	3
β-strand	603-604	2	23
β-strand	611-616	6	23
β-strand	621-631	11	23
β-strand	634-643	10	23
β-strand	646-649	4	23
β-strand	651-654	4	22
α-helix	660	1
β-strand	661	1	22
α-helix	662	1
β-strand	663	1	20
α-helix	666-667	2
β-strand	668-674	7	19
α-helix	675-677	3
α-helix	680-682	3
β-strand	685	1	24
α-helix	690-696	7
α-helix	699-701	3
α-helix	704-711	8
α-helix	713-719	7
α-helix	721-724	4
β-strand	727	1	24
α-helix	729-741	13
α-helix	756-758	3
α-helix	764-767	4
β-strand	770-773	4	19
α-helix	776-779	4
α-helix	791-794	4
β-strand	796-797	2	19
β-strand	803-805	3	19
α-helix	808-820	13
β-strand	823-824	2	19
α-helix	825	1
α-helix	829-832	4
α-helix	848-860	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle, intermediate form	A, C	protein	375	Oryctolagus cuniculus	P68135 (AlphaFold model)
Putative Adenylate cyclase,Profilin-1	B, D	protein	591	Vibrio nigripulchritudo SFn135	A0A9P1NJI6, P07737 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8BR0_1 Actin, alpha skeletal muscle, intermediate form (chains A, C)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Sequence of entity 2 (B, D), FASTA

>8BR0_2 Putative Adenylate cyclase,Profilin-1 (chains B, D)
GPGSQEATPNQDGSHKTYQSRDLVLEPIQHPKSIELGMPEVDQSVLAEVAERENVIIGVR
PVDEKSKSLIASKMYSSKGLFVKAKSSDWGPMSGFIPVDQSFAKASARRDLEKFNEYAEQ
SILSGNAVSANLYLNQVRIEELVSKYESLTPLELDVDSGMYKTTATNGDQTIPFFLNKVT
VDDKELWQVHYLREGELAPFKVIGDPVSKQPMTADYDLLTVMYTYGDLGPQDKVKQPLTW
EQWKESVTYEDLSPKYKARYDNQALYEKQDGASLGMVSDRLKELKDVINTSLGRTDGLEM
VHHGADDANPYAVMADNFPATFFVPKHFFDDDGLGEGKGSIQTYFNVNEQGAVVIQNPQE
FSNFQQVAINASYRASLNDKWNSGLDSPLFTTKRKLSHDYLDARDEVAKKLGLTESSKLN
GLGERQTMSPAQNSDVNTWARVDVSPPPPPGGAGWNAYIDNLMADGTCQDAAIVGYKDSP
SVWAAVPGKTFVNITPAEVGVLVGKDRSSFYVNGLTLGGQKCSVIRDSLLQDGEFSMDLR
TKSTGGAPTFNVTVTKTDKTLVLLMGKEGVHGGLINKKCYEMASHLRRSQY

Ligands and cofactors

ID	Name	Formula	Copies
CH1	3'-deoxy-cytidine-5'-triphosphate	C9 H16 N3 O13 P3	2
MN	Manganese (II) ion	Mn	6
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
LAB	Latrunculin B	C20 H29 N O5 S	2

Primary citation

Functional and structural insights into the multi-step activation and catalytic mechanism of bacterial ExoY nucleotidyl cyclase toxins bound to actin-profilin. Teixeira-Nunes, M., Retailleau, P., Raoux-Barbot, D. et al. PLoS Pathog (2023) 19:e1011654-e1011654. DOI 10.1371/journal.ppat.1011654 · PubMed

Other PDB entries of the same protein (UniProt P68135 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4B1Y 1.29 Å, Structure of the Phactr1 RPEL-3 bound to G-actin
2FXU 1.35 Å, X-ray Structure of Bistramide A- Actin Complex at 1.35 A resolution.
4K41 1.4 Å, Crystal structure of actin in complex with marine macrolide kabiramide C
1QZ5 1.45 Å, Structure of rabbit actin in complex with kabiramide C
1WUA 1.45 Å, The structure of Aplyronine A-actin complex
2Q0U 1.45 Å, Structure of Pectenotoxin-2 and Latrunculin B Bound to Actin
2V52 1.45 Å, Structure of MAL-RPEL2 complexed to G-actin
3MN5 1.5 Å, Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation
2PBD 1.5 Å, Ternary complex of profilin-actin with the poly-PRO-GAB domain of VASP*
5ZZA 1.53 Å, OdinProfilin/Rabbit Actin Complex
1J6Z 1.54 Å, Uncomplexed actin
1QZ6 1.6 Å, Structure of rabbit actin in complex with jaspisamide A

Browse structure collections

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