8BJJ: Actin, alpha skeletal muscle, intermediate form

Name: PDB 8BJJ: ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to ATP-Mg-actin, human profilin 1 and a sulfate ion
Published: 2023-09-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to ATP-Mg-actin, human profilin 1 and a sulfate ion. Determined by X-ray diffraction at 1.7 Å resolution. Released 20 Sept 2023.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Oryctolagus cuniculus, Homo sapiens, Vibrio nigripulchritudo
Chains: 3
Atoms: 7,763
Mol. weight: 104.96 kDa
Ligands: PEO, LAB, MG, ATP
Released: 20 Sept 2023

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

Secondary structure: helices and β-sheets

8BJJ contains 51 α-helices and 48 β-strands across 3 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: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-38	4	2
β-strand	53-54	2	2
α-helix	56-60	5
β-strand	65-68	4	2
β-strand	71-72	2	3
β-strand	75-76	2	3
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-125	13
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	182-194	13
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	5
β-strand	247-250	4	5
α-helix	253-262	10
α-helix	264-267	4
α-helix	271-273	3
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	335-337	3
α-helix	338-348	11
α-helix	350-354	5
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	369-373	5

Chain B: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	468-470	3	7
β-strand	473-475	3	7
α-helix	476-478	3
α-helix	490-503	14
β-strand	505-509	5	8
α-helix	510-513	4
α-helix	514-516	3
α-helix	517-521	5
β-strand	526-527	2	9
α-helix	535-537	3
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
β-strand	599	1	12
α-helix	600-602	3
β-strand	603-604	2	11
β-strand	611-614	4	11
β-strand	615	1	12
β-strand	623-631	9	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
β-strand	662-663	2	9
β-strand	668-674	7	8
α-helix	675-677	3
α-helix	729-742	14
α-helix	744-745	2
α-helix	764-766	3
β-strand	770-773	4	8
α-helix	776-779	4
α-helix	791-794	4
β-strand	796-797	2	8
β-strand	803-805	3	8
α-helix	808-820	13
β-strand	823-825	3	8
α-helix	843-845	3
α-helix	848-860	13

Chain C: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
β-strand	16-23	8	6
β-strand	29-33	5	6
α-helix	39-41	3
α-helix	44-51	8
α-helix	57-59	3
β-strand	63-65	3	6
β-strand	68-76	9	6
β-strand	84-89	6	6
β-strand	99-104	6	6
β-strand	108-114	7	6
α-helix	115	1
α-helix	120-136	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle, intermediate form	A	protein	375	Oryctolagus cuniculus	P68135 (AlphaFold model)
Profilin-1	C	protein	139	Homo sapiens	P07737 (AlphaFold model)
Putative Adenylate cyclase	B	protein	413	Vibrio nigripulchritudo	A0A9P1NJI6

Sequence of entity 1 (A), FASTA

>8BJJ_1 Actin, alpha skeletal muscle, intermediate form (chains A)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Sequence of entity 2 (C), FASTA

>8BJJ_2 Profilin-1 (chains C)
AGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGVLVGKDRSSFYV
NGLTLGGQKCSVIRDSLLQDGEFSMDLRTKSTGGAPTFNVTVTKTDKTLVLLMGKEGVHG
GLINKKCYEMASHLRRSQY

Sequence of entity 3 (B), FASTA

>8BJJ_3 Putative Adenylate cyclase (chains B)
GPGSQEATPNQDGSHKTYQSRDLVLEPIQHPKSIELGMPEVDQSVLAEVAERENVIIGVR
PVDEKSKSLIASKMYSSKGLFVKAKSSDWGPMSGFIPVDQSFAKASARRDLEKFNEYAEQ
SILSGNAVSANLYLNQVRIEELVSKYESLTPLELDVDSGMYKTTATNGDQTIPFFLNKVT
VDDKELWQVHYLREGELAPFKVIGDPVSKQPMTADYDLLTVMYTYGDLGPQDKVKQPLTW
EQWKESVTYEDLSPKYKARYDNQALYEKQDGASLGMVSDRLKELKDVINTSLGRTDGLEM
VHHGADDANPYAVMADNFPATFFVPKHFFDDDGLGEGKGSIQTYFNVNEQGAVVIQNPQE
FSNFQQVAINASYRASLNDKWNSGLDSPLFTTKRKLSHDYLDARDEVAKKLGL

Ligands and cofactors

ID	Name	Formula	Copies
PEO	Hydrogen peroxide	H2 O2	2
LAB	Latrunculin B	C20 H29 N O5 S	1
MG	Magnesium ion	Mg	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Water and common crystallization additives (GOL, SO4, TRS, PG4) are not listed.

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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