SAXSdb — 9duu

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

Actin, alpha skeletal muscle

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count	Chain A； UniProt 3–377 Chain B； UniProt 3–377 Chain C； UniProt 3–377 Chain D； UniProt 3–377 Chain E； UniProt 3–377 Chain F； UniProt 3–377	Non-standard monomer：Yes (specific site not provided by mmCIF)	phalloidin × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7；25 mM KCl, 2 mM EGTA, 60 mM MOPS (pH7), 1 mM DTT, and 4 mM MgCl2 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9DUU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7RNS nSH2 domain of p85-alpha subunit of phosphatidylinositol 3-kinase in complex with an actin peptide with phosphorylated tyrosine 53 Deposited 2021-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 52–60（9 aa） Fragment：UNP residues 52-60	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.05 M cadmium sulfate hydrate, 0.1 M HEPES, pH 7.5, 1.0 M sodium acetate trihydrate	Resolution 1.14 Å R-free 0.147
7RNU nSH2 domain of p85-beta subunit of phosphatidylinositol 3-kinase in complex with an actin peptide with phosphorylated tyrosine 53 Deposited 2021-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 52–60（9 aa） Fragment：UNP residues 52-60	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；292 K；25% w/v PEG1500, 100 mM MIB, pH 5.0	Resolution 1.45 Å R-free 0.222
7RNU nSH2 domain of p85-beta subunit of phosphatidylinositol 3-kinase in complex with an actin peptide with phosphorylated tyrosine 53 Deposited 2021-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 52–60（9 aa） Fragment：UNP residues 52-60	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；292 K；25% w/v PEG1500, 100 mM MIB, pH 5.0	Resolution 1.45 Å R-free 0.222
7RNU nSH2 domain of p85-beta subunit of phosphatidylinositol 3-kinase in complex with an actin peptide with phosphorylated tyrosine 53 Deposited 2021-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 52–60（9 aa） Fragment：UNP residues 52-60	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；292 K；25% w/v PEG1500, 100 mM MIB, pH 5.0	Resolution 1.45 Å R-free 0.222
7RNU nSH2 domain of p85-beta subunit of phosphatidylinositol 3-kinase in complex with an actin peptide with phosphorylated tyrosine 53 Deposited 2021-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 52–60（9 aa） Fragment：UNP residues 52-60	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；292 K；25% w/v PEG1500, 100 mM MIB, pH 5.0	Resolution 1.45 Å R-free 0.222
7RNV SH2 domain of guanine nucleotide exchange factor Vav2 in complex with an actin peptide with phosphorylated tyrosine 53 Deposited 2021-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 52–60（9 aa） Fragment：UNP residues 52-60	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；0.2 M sodium acetate trihydrate, 0.1 M Tris hydrochloride, pH 8.5, 30% PEG4000	Resolution 2.15 Å R-free 0.272
9DUV Cryo-EM structure of recombinant R254H ACTA1 phalloidin-stabilized F-actin Deposited 2024-10-04	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 3–377（375 aa） Chain B 3–377（375 aa） Chain C 3–377（375 aa） Chain D 3–377（375 aa） Chain E 3–377（375 aa） Chain F 3–377（375 aa）	Mutation：R254H Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R254H Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R254H Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R254H Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R254H Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R254H Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7；25 mM KCl, 2 mM EGTA, 60 mM MOPS (pH7), 1 mM DTT, and 4 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ACTS_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–375； UniProt 3–377 Author chain B； PDBConstruct 1–375； UniProt 3–377 Author chain C； PDBConstruct 1–375； UniProt 3–377 Author chain D； PDBConstruct 1–375； UniProt 3–377 Author chain E； PDBConstruct 1–375； UniProt 3–377 Author chain F； PDBConstruct 1–375； UniProt 3–377

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	9duu
Deposition date deposition_date	2024-10-04
Structure title title	Cryo-EM structure of recombinant wildtype ACTA1 phalloidin-stabilized F-actin
Keywords keywords	Actin, cardiomyopathy, contractility, muscle, sarcomere, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	53.35 Å
Radius of gyration Rg (electron density) rg_electron	54.16 Å
Forward intensity I(0) i0	968221000.00
Molecular weight molecular_weight	256280.0 kDa
Excluded volume excluded_volume	319660 Å³
Envelope volume envelope_volume	425150 Å³
Hydration-shell volume shell_volume	71418 Å³
Envelope diameter envelope_diameter	213.3 Å
Shell Rg shell_rg	49.79 Å
Envelope Rg envelope_rg	54.25 Å
Shape Rg shape_rg	54.17 Å
Total Rg total_rg	54.00 Å
Total atoms total_atoms	17953
Residues n_residues	2248
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	194.1 Å
Rg (real space) rg_real	54.00 Å
Rg uncertainty (real space) rg_real_error	2.36 Å
I(0) (real space) i0_real	9.6820e+08
I(0) uncertainty (real space) i0_real_error	2.3930e+07
Rg (reciprocal space) rg_reciprocal	52.80 Å
I(0) (reciprocal space) i0_reciprocal	966600000.0000
Solution quality estimate total_estimate	0.7610
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	46.9 Å
Skewness Skewness skewness	0.686
Kurtosis Kurtosis kurtosis	-0.106
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	70900000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.515; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.775; Smooth: 0.567

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Actin, alpha skeletal muscle
Molecular weight formula_weight	41875.6 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	17953

DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	phalloidin
Molecular weight formula_weight	808.9 kDa
Source method src_method	syn
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O,P,Q,R,S

WXATCPA

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	3.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	1574745

fit	/app/data/saxs_computation/du/9duu/9duu.fit
pddf	/app/data/pr_computation/du/9duu/9duu.pr.out
profile	/app/data/saxs_computation/du/9duu/9duu.dat

Cryo-EM structure of recombinant wildtype ACTA1 phalloidin-stabilized F-actin

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

Actin, alpha skeletal muscle

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)