1nlv

Crystal Structure Of Dictyostelium Discoideum Actin Complexed With Ca ATP And Human Gelsolin Segment 1

Method: X-RAY DIFFRACTION Dmax: 82.2 Å Quality: GOOD

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

Actin

OrganismNot specified

UniProt P02577

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 1–375 Not recorded Gelsolin × 1 (P06396) CA CALCIUM ION × 2 SO4 SULFATE ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO2 SULFUR DIOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;lithium chloride, magnesium chloride, HEPES, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.80 Å R-free 0.258
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–375 Not recorded Gelsolin × 2 (P06396) CA CALCIUM ION × 4 SO4 SULFATE ION × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 SO2 SULFUR DIOXIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;lithium chloride, magnesium chloride, HEPES, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.80 Å R-free 0.258

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.

2 other PDB entries and 4 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 1–375

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:DOMAIN 1 Actin × 1 (P02577) CA CALCIUM ION × 2 SO4 SULFATE ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO2 SULFUR DIOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;lithium chloride, magnesium chloride, HEPES, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.80 Å R-free 0.258
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 52–176 Fragment:DOMAIN 1 Actin × 2 (P02577) CA CALCIUM ION × 4 SO4 SULFATE ION × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 SO2 SULFUR DIOXIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;lithium chloride, magnesium chloride, HEPES, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.80 Å R-free 0.258

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 1–125; 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 1nlv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1nlv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1nlv
Deposition date deposition_date2003-01-07
Structure title titleCrystal Structure Of Dictyostelium Discoideum Actin Complexed With Ca ATP And Human Gelsolin Segment 1
Keywords keywordsactin, gelsolin, cytoskeleton, cell motility, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.87
Radius of gyration Rg (electron density) rg_electron24.01
Forward intensity I(0) i049843100.00
Molecular weight molecular_weight54328.0 kDa
Excluded volume excluded_volume67706 ų
Envelope volume envelope_volume79006 ų
Hydration-shell volume shell_volume27475 ų
Envelope diameter envelope_diameter83.0
Shell Rg shell_rg31.28
Envelope Rg envelope_rg24.36
Shape Rg shape_rg24.05
Total Rg total_rg24.72
Total atoms total_atoms3815
Residues n_residues487
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 dmax82.2
Rg (real space) rg_real24.82
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real4.9840e+07
I(0) uncertainty (real space) i0_real_error7.2370e+05
Rg (reciprocal space) rg_reciprocal24.84
I(0) (reciprocal space) i0_reciprocal49840000.0000
Solution quality estimate total_estimate0.8899
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.7
Skewness Skewness skewness0.317
Kurtosis Kurtosis kurtosis-0.324
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha13320000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.977

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1nlva1
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_idd1nlva2
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_idd1nlvg_
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

CATH v4.4 (4 domains)

Domain ID domain_id1nlvA01
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_id1nlvA02
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_id1nlvA03
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_id1nlvG00
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)