SAXSdb — 8dnf

▼

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

Actin, cytoplasmic 2, N-terminally processed

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–375 Chain B； UniProt 2–375 Chain C； UniProt 2–375 Chain D； UniProt 2–375	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.38 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 8DNF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5JLH Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution Deposited 2016-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 2–375（374 aa） Chain B 2–375（374 aa） Chain C 2–375（374 aa） Chain D 2–375（374 aa） Chain E 2–375（374 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；5 mM Tris-HCl pH 7.5, 1 mM DTT, 100 mM KCl, and 2 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE；Sample (2 uL of F-actin-tropomyosin solution) was applied to a glow-discharged holey carbon grid, incubated for 20 s and manually blotted from the backside for less than a second with filter paper. Afterwards 1.5 uL of myosin solution (3 uM without nucleotide) were added directly on the grid, incubated for 10 s and then manually blotted for 5 s from the backside with filter paper.	Resolution 3.90 Å
6CXI Cardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C mode 1 Deposited 2018-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 1–375（375 aa） Chain B 1–375（375 aa） Chain C 1–375（375 aa） Chain D 1–375（375 aa） Chain E 1–375（375 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.00 Å
6CXJ Cardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C mode 2 Deposited 2018-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 1–375（375 aa） Chain B 1–375（375 aa） Chain C 1–375（375 aa） Chain D 1–375（375 aa） Chain E 1–375（375 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.00 Å
6G2T human cardiac myosin binding protein C C1 Ig-domain bound to native cardiac thin filament Deposited 2018-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–375（375 aa） Chain B 1–375（375 aa） Chain C 1–375（375 aa） Chain D 1–375（375 aa） Chain E 1–375（375 aa） Chain F 1–375（375 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
6WK1 SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine Deposited 2020-04-15	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 × 4 PDB declaration: tetrameric	Chain Y 66–88（23 aa） Chain Z 66–88（23 aa）	Mutation：H73M Mutation：H73M	GOL GLYCEROL × 6 EDO 1,2-ETHANEDIOL × 46 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.89 Å R-free 0.228
6WK1 SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine Deposited 2020-04-15	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 Y 66–88（23 aa）	Mutation：H73M	GOL GLYCEROL × 6 EDO 1,2-ETHANEDIOL × 27 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.89 Å R-free 0.228
6WK1 SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine Deposited 2020-04-15	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 Z 66–88（23 aa）	Mutation：H73M	EDO 1,2-ETHANEDIOL × 19 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.89 Å R-free 0.228
6WK2 SETD3 mutant (N255V) in Complex with an Actin Peptide with His73 Replaced with Methionine Deposited 2020-04-15	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 × 4 PDB declaration: tetrameric	Chain C 66–88（23 aa） Chain Y 66–88（23 aa）	Mutation：H73M Mutation：H73M	SAM S-ADENOSYLMETHIONINE × 2 EDO 1,2-ETHANEDIOL × 8 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.76 Å R-free 0.206
6WK2 SETD3 mutant (N255V) in Complex with an Actin Peptide with His73 Replaced with Methionine Deposited 2020-04-15	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 Y 66–88（23 aa）	Mutation：H73M	SAM S-ADENOSYLMETHIONINE × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.76 Å R-free 0.206
6WK2 SETD3 mutant (N255V) in Complex with an Actin Peptide with His73 Replaced with Methionine Deposited 2020-04-15	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 C 66–88（23 aa）	Mutation：H73M	SAM S-ADENOSYLMETHIONINE × 1 EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.76 Å R-free 0.206
7NVM Human TRiC complex in closed state with nanobody Nb18, actin and PhLP2A bound Deposited 2021-03-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain K 1–375（375 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 16 MG MAGNESIUM ION × 16 AF3 ALUMINUM FLUORIDE × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9SMX CM1-activated gTuRC in complex with nascent alpha-E254D mutant microtubules Deposited 2025-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 73 PDB declaration: 73-meric	Chain 7 2–375（374 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.67 Å

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ACTG_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–375； UniProt 2–375 Author chain B； PDBConstruct 2–375； UniProt 2–375 Author chain C； PDBConstruct 2–375； UniProt 2–375 Author chain D； PDBConstruct 2–375； UniProt 2–375

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8dnf
Deposition date deposition_date	2022-07-11
最后修订 last_revision	2023-04-12
Structure title title	Cryo-EM structure of nonmuscle gamma-actin
Keywords keywords	cytoskeleton, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	42.62 Å
Radius of gyration Rg (electron density) rg_electron	42.66 Å
Forward intensity I(0) i0	435835000.00
Molecular weight molecular_weight	168640.0 kDa
Excluded volume excluded_volume	210220 Å³
Envelope volume envelope_volume	300500 Å³
Hydration-shell volume shell_volume	60738 Å³
Envelope diameter envelope_diameter	162.8 Å
Shell Rg shell_rg	45.70 Å
Envelope Rg envelope_rg	42.46 Å
Shape Rg shape_rg	42.68 Å
Total Rg total_rg	42.76 Å
Total atoms total_atoms	11812
Residues n_residues	1492
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

▼

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

Maximum dimension Dmax dmax	152.2 Å
Rg (real space) rg_real	42.83 Å
Rg uncertainty (real space) rg_real_error	1.89 Å
I(0) (real space) i0_real	4.3580e+08
I(0) uncertainty (real space) i0_real_error	7.7600e+06
Rg (reciprocal space) rg_reciprocal	42.62 Å
I(0) (reciprocal space) i0_reciprocal	435700000.0000
Solution quality estimate total_estimate	0.8465
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.2 Å
Skewness Skewness skewness	0.540
Kurtosis Kurtosis kurtosis	-0.015
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	60520000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.734; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.839

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Actin, cytoplasmic 2, N-terminally processed
Molecular weight formula_weight	41746.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11812

XEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF

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	Pichia

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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	4

▶

8. Citations (1)

▶

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	3.38 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	1009372

fit	/app/data/saxs_computation/dn/8dnf/8dnf.fit
pddf	/app/data/pr_computation/dn/8dnf/8dnf.pr.out
profile	/app/data/saxs_computation/dn/8dnf/8dnf.dat

Cryo-EM structure of nonmuscle gamma-actin

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

Actin, cytoplasmic 2, N-terminally processed

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