7k21

Cryo-EM structure of pyrene-labeled ADP-Pi-actin filaments

Method: ELECTRON MICROSCOPY Dmax: 144.1 Å Quality: GOOD

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

Actin, alpha skeletal muscle

OrganismNot specified

UniProt P68139

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 3–377 Chain B; UniProt 3–377 Chain C; UniProt 3–377 Chain D; UniProt 3–377 Non-standard monomer:Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4 PO4 PHOSPHATE ION × 4 1T4 N-(pyren-1-yl)acetamide × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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.

57 other PDB entries and 66 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACTS_CHICK
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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 7k21

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7k21
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7k21
Deposition date deposition_date2020-09-08
Structure title titleCryo-EM structure of pyrene-labeled ADP-Pi-actin filaments
Keywords keywordsactin, pyrene, fluorescence, ADP, phosphate, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier40.56
Radius of gyration Rg (electron density) rg_electron40.60
Forward intensity I(0) i0436645000.00
Molecular weight molecular_weight169070.0 kDa
Excluded volume excluded_volume210710 ų
Envelope volume envelope_volume268070 ų
Hydration-shell volume shell_volume56842 ų
Envelope diameter envelope_diameter154.2
Shell Rg shell_rg44.44
Envelope Rg envelope_rg40.49
Shape Rg shape_rg40.62
Total Rg total_rg40.75
Total atoms total_atoms11848
Residues n_residues1484
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax144.1
Rg (real space) rg_real40.74
Rg uncertainty (real space) rg_real_error1.55
I(0) (real space) i0_real4.3660e+08
I(0) uncertainty (real space) i0_real_error8.2550e+06
Rg (reciprocal space) rg_reciprocal40.56
I(0) (reciprocal space) i0_reciprocal436600000.0000
Solution quality estimate total_estimate0.8407
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.3
Skewness Skewness skewness0.548
Kurtosis Kurtosis kurtosis0.000
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha47280000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.740; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.821

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd7k21a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.0 — automated matches
Domain ID domain_idd7k21a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.1 — Actin/HSP70
Domain ID domain_idd7k21b1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.0 — automated matches
Domain ID domain_idd7k21b2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.1 — Actin/HSP70
Domain ID domain_idd7k21c1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.0 — automated matches
Domain ID domain_idd7k21c2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.1 — Actin/HSP70
Domain ID domain_idd7k21d1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.0 — automated matches
Domain ID domain_idd7k21d2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.1 — Actin/HSP70

8. Citations (1)

9. Files and Curves (10)