8BJI: Actin, alpha skeletal muscle, intermediate form

Name: PDB 8BJI: chimera of ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo fused to a proline-Rich-Domain (PRD) and profilin, bound to ADP-Mg-actin and a sulfate ion
Published: 2023-09-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

chimera of ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo fused to a proline-Rich-Domain (PRD) and profilin, bound to ADP-Mg-actin and a sulfate ion. Determined by X-ray diffraction at 1.75 Å resolution. Released 20 Sept 2023.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Oryctolagus cuniculus, Vibrio nigripulchritudo, Homo sapiens
Chains: 2
Atoms: 7,926
Mol. weight: 109.14 kDa
Ligands: ADP, MG, PEO
Released: 20 Sept 2023

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

Secondary structure: helices and β-sheets

8BJI contains 49 α-helices and 48 β-strands across 2 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: 22 helices, 17 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	35-38	4	2
β-strand	53-54	2	2
α-helix	56-60	5
β-strand	65-68	4	2
α-helix	79-87	9
α-helix	88-93	6
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	3
β-strand	160-166	7	3
β-strand	169-170	2	3
α-helix	172-174	3
β-strand	176-178	3	3
α-helix	182-194	13
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	4
β-strand	247-250	4	4
α-helix	253-262	10
α-helix	264-267	4
α-helix	271-273	3
α-helix	274-284	11
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	3
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	3
α-helix	338-347	10
α-helix	352-355	4
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	369-373	5

Chain B: 27 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	468-470	3	5
β-strand	473-475	3	5
α-helix	481-483	3
α-helix	490-503	14
β-strand	505-509	5	6
α-helix	514-516	3
α-helix	517-521	5
β-strand	526-527	2	7
α-helix	535-536	2
β-strand	537	1	8
β-strand	543	1	8
β-strand	547	1	9
α-helix	550-552	3
α-helix	555-558	4
α-helix	561-573	13
β-strand	578-581	4	9
β-strand	583-584	2	10
α-helix	586-590	5
α-helix	591-595	5
β-strand	599	1	11
α-helix	600-602	3
β-strand	603-605	3	10
β-strand	610-614	5	10
β-strand	615	1	11
β-strand	623-631	9	10
β-strand	634-643	10	10
β-strand	646-649	4	10
β-strand	651-654	4	9
α-helix	660	1
β-strand	661	1	9
β-strand	662-663	2	7
β-strand	668-673	6	6
α-helix	675-677	3
α-helix	729-742	14
α-helix	744-745	2
α-helix	764-767	4
β-strand	770-773	4	6
α-helix	776-779	4
α-helix	791-794	4
β-strand	796-797	2	6
β-strand	803-805	3	6
α-helix	808-820	13
β-strand	824-825	2	6
α-helix	848-860	13
α-helix	896-899	4
α-helix	906-913	8
β-strand	918-925	8	12
β-strand	931-935	5	12
α-helix	941-943	3
α-helix	946-953	8
α-helix	959-961	3
β-strand	965-967	3	12
β-strand	970-978	9	12
β-strand	986-991	6	12
β-strand	1001-1006	6	12
β-strand	1010-1016	7	12
α-helix	1017	1
α-helix	1022-1038	17

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>8BJI_1 Actin, alpha skeletal muscle, intermediate form (chains A)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Sequence of entity 2 (B), FASTA

>8BJI_2 Putative Adenylate cyclase,Profilin-1 (chains B)
GPGSQEATPNQDGSHKTYQSRDLVLEPIQHPKSIELGMPEVDQSVLAEVAERENVIIGVR
PVDEKSKSLIASKMYSSKGLFVKAKSSDWGPMSGFIPVDQSFAKASARRDLEKFNEYAEQ
SILSGNAVSANLYLNQVRIEELVSKYESLTPLELDVDSGMYKTTATNGDQTIPFFLNKVT
VDDKELWQVHYLREGELAPFKVIGDPVSKQPMTADYDLLTVMYTYGDLGPQDKVKQPLTW
EQWKESVTYEDLSPKYKARYDNQALYEKQDGASLGMVSDRLKELKDVINTSLGRTDGLEM
VHHGADDANPYAVMADNFPATFFVPKHFFDDDGLGEGKGSIQTYFNVNEQGAVVIQNPQE
FSNFQQVAINASYRASLNDKWNSGLDSPLFTTKRKLSHDYLDARDEVAKKLGLTESSKLN
GLGERQTMSPAQNSDVNTWARVDVSPPPPPGGAGWNAYIDNLMADGTCQDAAIVGYKDSP
SVWAAVPGKTFVNITPAEVGVLVGKDRSSFYVNGLTLGGQKCSVIRDSLLQDGEFSMDLR
TKSTGGAPTFNVTVTKTDKTLVLLMGKEGVHGGLINKKCYEMASHLRRSQY

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	1
PEO	Hydrogen peroxide	H2 O2	14

Water and common crystallization additives (TRS, GOL, PEG, SO4) 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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