8bjj

ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to ATP-Mg-actin, human profilin 1 and a sulfate ion

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	Protein heterocomplex	Heteromer	Protein 3	Profilin-1 × 1 （P07737） Putative Adenylate cyclase × 1 （A0A6N3LUE9） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 LATRUNCULIN B × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 SULFATE ION × 4 HYDROGEN PEROXIDE × 2 TETRAETHYLENE GLYCOL × 1 GLYCEROL × 1 water × 3	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

Profilin-1

Homo sapiens

UniProt P07737

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Actin, alpha skeletal muscle, intermediate form × 1 （P68135） Putative Adenylate cyclase × 1 （A0A6N3LUE9） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 LATRUNCULIN B × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 SULFATE ION × 4 HYDROGEN PEROXIDE × 2 TETRAETHYLENE GLYCOL × 1 GLYCEROL × 1 water × 3	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 C； PDBConstruct 1–139； UniProt 2–140

Putative Adenylate cyclase

Vibrio nigripulchritudo

UniProt A0A6N3LUE9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Actin, alpha skeletal muscle, intermediate form × 1 （P68135） Profilin-1 × 1 （P07737） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 LATRUNCULIN B × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 SULFATE ION × 4 HYDROGEN PEROXIDE × 2 TETRAETHYLENE GLYCOL × 1 GLYCEROL × 1 water × 3	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	3
Chains and sequence ranges	Author chain B； PDBConstruct 5–413； UniProt 3455–3863

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	8bjj
Deposition date deposition_date	2022-11-04
Structure title title	ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to ATP-Mg-actin, human profilin 1 and a sulfate ion
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.

8bjj__assembly_1__model_1

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

Download this curve (.dat)

8bjj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8bjj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.80 Å
Rg (electron density)	33.83 Å
Total Rg	34.12 Å
Atom count	6836
Residues	861
Excluded volume	121470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8bjj__assembly_1__model_1`	trimeric （3）	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 (12)

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7763

DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF

Entity 2 Entity 2 polymer

Description description	Profilin-1
Molecular weight formula_weight	14940.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

AGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGVLVGKDRSSFYVNGLTLGGQKCSVIRDSLLQDGEFSMDLRTKSTGGAPTFNVTVTKTDKTLVLLMGKEGVHGGLINKKCYEMASHLRRSQY

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Putative Adenylate cyclase
Molecular weight formula_weight	46247.5 kDa
EC 编号 ec_number	4.6.1.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPGSQEATPNQDGSHKTYQSRDLVLEPIQHPKSIELGMPEVDQSVLAEVAERENVIIGVRPVDEKSKSLIASKMYSSKGLFVKAKSSDWGPMSGFIPVDQSFAKASARRDLEKFNEYAEQSILSGNAVSANLYLNQVRIEELVSKYESLTPLELDVDSGMYKTTATNGDQTIPFFLNKVTVDDKELWQVHYLREGELAPFKVIGDPVSKQPMTADYDLLTVMYTYGDLGPQDKVKQPLTWEQWKESVTYEDLSPKYKARYDNQALYEKQDGASLGMVSDRLKELKDVINTSLGRTDGLEMVHHGADDANPYAVMADNFPATFFVPKHFFDDDGLGEGKGSIQTYFNVNEQGAVVIQNPQEFSNFQQVAINASYRASLNDKWNSGLDSPLFTTKRKLSHDYLDARDEVAKKLGL

Source Source

Source organism organism	Vibrio nigripulchritudo
NCBI taxonomy ID ncbi_taxonomy_id	28173
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	LATRUNCULIN B
Molecular weight formula_weight	395.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 non-polymer

Description description	HYDROGEN PEROXIDE
Molecular weight formula_weight	34.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	722

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Unit-cell length a length_a	81.186 Å
Unit-cell length b length_b	63.202 Å
Unit-cell length c length_c	93.455 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.04 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.699 Å
Low-resolution limit resolution_low	44.200 Å
R factor r_factor	0.1761
R_work r_work	0.1751
R_free r_free	0.1949

ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to ATP-Mg-actin, human profilin 1 and a sulfate ion

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

Profilin-1

State in the Current Structure

Other States of the Same Protein in the Database

Putative Adenylate cyclase

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

8bjj__assembly_1__model_1

8bjj__assembly_1__model_1 | I(q)

8bjj__assembly_1__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

7. Citations (1)

ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to ATP-Mg-actin, human profilin 1 and a sulfate ion

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

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

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

8bjj__assembly_1__model_1

8bjj__assembly_1__model_1 | I(q)

8bjj__assembly_1__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

7. Citations (1)