3ci5

Complex of Phosphorylated Dictyostelium Discoideum Actin with Gelsolin

Method: X-RAY DIFFRACTION Dmax: 84.1 Å Quality: REASONABLE

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

Major actin

OrganismNot specified

UniProt P07830

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–376 Non-standard monomer:Yes (specific site not provided by mmCIF) Gelsolin × 1 (P06396) MG MAGNESIUM ION × 1 SO4 SULFATE ION × 10 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 5 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.1M HEPES, 1.7M Li2SO4, 2mM ATP, 1mM EDTA, 10% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.70 Å R-free 0.191
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 2–376 Non-standard monomer:Yes (specific site not provided by mmCIF) Gelsolin × 2 (P06396) MG MAGNESIUM ION × 2 SO4 SULFATE ION × 20 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 GOL GLYCEROL × 10 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.1M HEPES, 1.7M Li2SO4, 2mM ATP, 1mM EDTA, 10% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.70 Å R-free 0.191

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.

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACT1_DICDI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–375; UniProt 2–376

Gelsolin

Homo sapiens

UniProt P06396

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 52–176 Fragment:Gelsolin Segment 1 (UNP residues 52-176) Major actin × 1 (P07830) MG MAGNESIUM ION × 1 SO4 SULFATE ION × 10 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 5 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.1M HEPES, 1.7M Li2SO4, 2mM ATP, 1mM EDTA, 10% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.70 Å R-free 0.191
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 52–176 Fragment:Gelsolin Segment 1 (UNP residues 52-176) Major actin × 2 (P07830) MG MAGNESIUM ION × 2 SO4 SULFATE ION × 20 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 GOL GLYCEROL × 10 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.1M HEPES, 1.7M Li2SO4, 2mM ATP, 1mM EDTA, 10% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.70 Å R-free 0.191

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.

60 other PDB entries and 93 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GELS_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain G; PDBConstruct 2–126; UniProt 52–176

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 3ci5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3ci5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3ci5
Deposition date deposition_date2008-03-10
Structure title titleComplex of Phosphorylated Dictyostelium Discoideum Actin with Gelsolin
Keywords keywords;Actin, Gelsolin, Dictyostelium discoideum, Phosphorylated Tyrosine, Actin-Associated Protein, Methyl Histidine, ATP-binding, Cytoskeleton, Nucleotide-binding, Phosphoprotein, Structural protein, Actin capping, Actin-binding, Alternative initiation, Amyloid, Disease mutation, Secreted ;; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.26
Radius of gyration Rg (electron density) rg_electron24.38
Forward intensity I(0) i057281000.00
Molecular weight molecular_weight57182.0 kDa
Excluded volume excluded_volume70734 ų
Envelope volume envelope_volume84104 ų
Hydration-shell volume shell_volume28629 ų
Envelope diameter envelope_diameter87.8
Shell Rg shell_rg31.84
Envelope Rg envelope_rg24.84
Shape Rg shape_rg24.39
Total Rg total_rg25.14
Total atoms total_atoms3996
Residues n_residues492
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 dmax84.1
Rg (real space) rg_real25.22
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real5.7280e+07
I(0) uncertainty (real space) i0_real_error8.0860e+05
Rg (reciprocal space) rg_reciprocal25.23
I(0) (reciprocal space) i0_reciprocal57280000.0000
Solution quality estimate total_estimate0.6848
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.4
Skewness Skewness skewness0.320
Kurtosis Kurtosis kurtosis-0.299
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14190000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 0.120; Positv: 1.000; Valcen: 0.982; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3ci5a1
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_idd3ci5a2
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_idd3ci5g2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.109 — Gelsolin-like
Superfamily Superfamily superfamilyd.109.1 — Actin depolymerizing proteins
Family Family familyd.109.1.1 — Gelsolin-like
Domain ID domain_idd3ci5g3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id3ci5A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id3ci5A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id3ci5A03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily10 — ATPase, substrate binding domain, subdomain 4
Domain ID domain_id3ci5G00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology20 — Severin
Homologous superfamily homologous superfamily10 — Severin

8. Citations (1)

9. Files and Curves (10)