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

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin, alpha skeletal muscle, intermediate form

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Putative Adenylate cyclase,Profilin-1 × 1 （A0A6N3LUE9,P07737） LATRUNCULIN B × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MANGANESE (II) ION × 3 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Putative Adenylate cyclase,Profilin-1 × 1 （A0A6N3LUE9,P07737） LATRUNCULIN B × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MANGANESE (II) ION × 3 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACTS_RABIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–375； UniProt 3–377 Author chain C； PDBConstruct 1–375； UniProt 3–377

Putative Adenylate cyclase,Profilin-1

Vibrio nigripulchritudo SFn135

UniProt A0A6N3LUE9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Actin, alpha skeletal muscle, intermediate form × 1 （P68135） LATRUNCULIN B × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MANGANESE (II) ION × 3 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Actin, alpha skeletal muscle, intermediate form × 1 （P68135） LATRUNCULIN B × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MANGANESE (II) ION × 3 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6N3LUE9_9VIBR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–446； UniProt 3455–3896 Author chain D； PDBConstruct 5–446； UniProt 3455–3896

Putative Adenylate cyclase,Profilin-1

Vibrio nigripulchritudo SFn135

UniProt P07737

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Actin, alpha skeletal muscle, intermediate form × 1 （P68135） LATRUNCULIN B × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MANGANESE (II) ION × 3 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Actin, alpha skeletal muscle, intermediate form × 1 （P68135） LATRUNCULIN B × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MANGANESE (II) ION × 3 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PROF1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 453–591； UniProt 2–140 Author chain D； PDBConstruct 453–591； UniProt 2–140

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8br0
Deposition date deposition_date	2022-11-22
Structure title title	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
Keywords keywords	bacterial nucleotidyl cyclase toxin, activated complex, Toxin; TOXIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8br0__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8br0__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8br0__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	30.08 Å
Rg (electron density)	29.67 Å
Total Rg	30.23 Å
Atom count	6089
Residues	763
Excluded volume	108050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8br0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8br0__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Actin, alpha skeletal muscle, intermediate form
Molecular weight formula_weight	41862.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	12638

DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF

Entity 2 Entity 2 polymer

Description description	Putative Adenylate cyclase,Profilin-1
Molecular weight formula_weight	65232.9 kDa
EC 编号 ec_number	4.6.1.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GPGSQEATPNQDGSHKTYQSRDLVLEPIQHPKSIELGMPEVDQSVLAEVAERENVIIGVRPVDEKSKSLIASKMYSSKGLFVKAKSSDWGPMSGFIPVDQSFAKASARRDLEKFNEYAEQSILSGNAVSANLYLNQVRIEELVSKYESLTPLELDVDSGMYKTTATNGDQTIPFFLNKVTVDDKELWQVHYLREGELAPFKVIGDPVSKQPMTADYDLLTVMYTYGDLGPQDKVKQPLTWEQWKESVTYEDLSPKYKARYDNQALYEKQDGASLGMVSDRLKELKDVINTSLGRTDGLEMVHHGADDANPYAVMADNFPATFFVPKHFFDDDGLGEGKGSIQTYFNVNEQGAVVIQNPQEFSNFQQVAINASYRASLNDKWNSGLDSPLFTTKRKLSHDYLDARDEVAKKLGLTESSKLNGLGERQTMSPAQNSDVNTWARVDVSPPPPPGGAGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGVLVGKDRSSFYVNGLTLGGQKCSVIRDSLLQDGEFSMDLRTKSTGGAPTFNVTVTKTDKTLVLLMGKEGVHGGLINKKCYEMASHLRRSQY

Source Source

Source organism organism	Vibrio nigripulchritudo SFn135
NCBI taxonomy ID ncbi_taxonomy_id	1238448
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	LATRUNCULIN B
Molecular weight formula_weight	395.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	467.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	541

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Unit-cell length a length_a	74.469 Å
Unit-cell length b length_b	132.503 Å
Unit-cell length c length_c	96.217 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.218 Å
Low-resolution limit resolution_low	48.050 Å
R factor r_factor	0.2102
R_work r_work	0.2085
R_free r_free	0.2428

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin, alpha skeletal muscle, intermediate form

State in the Current Structure

Other States of the Same Protein in the Database

Putative Adenylate cyclase,Profilin-1

State in the Current Structure

Other States of the Same Protein in the Database

Putative Adenylate cyclase,Profilin-1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8br0__assembly_2__model_1

8br0__assembly_2__model_1 | I(q)

8br0__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin, alpha skeletal muscle, intermediate form

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Putative Adenylate cyclase,Profilin-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Putative Adenylate cyclase,Profilin-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8br0__assembly_2__model_1

8br0__assembly_2__model_1 | I(q)

8br0__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)