1t44

Structural basis of actin sequestration by thymosin-B4: Implications for arp2/3 activation

Method: X-RAY DIFFRACTION Dmax: 84.9 Å Quality: GOOD

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

Chimera of Gelsolin domain 1 and C-Terminal domain of thymosin Beta-4

Mus musculus

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 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 55–179 Fragment:Chimera of Gelsolin domain 1 (residues 28-152) from human and C-Terminal domain of thymosin Beta-4 from mouse (residues 153-171) Actin, alpha × 1 (P02568) CA CALCIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 6.5;293 K;PEG 8000, Sodium acetate, calcium chloride, pH 6.5, microbatch, temperature 293K Resolution 2.00 Å R-free 0.195

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 94 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GELS_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain G; PDBConstruct 4–128; UniProt 55–179

Chimera of Gelsolin domain 1 and C-Terminal domain of thymosin Beta-4

Mus musculus

UniProt P20065

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 28–46 Fragment:Chimera of Gelsolin domain 1 (residues 28-152) from human and C-Terminal domain of thymosin Beta-4 from mouse (residues 153-171) Actin, alpha × 1 (P02568) CA CALCIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 6.5;293 K;PEG 8000, Sodium acetate, calcium chloride, pH 6.5, microbatch, temperature 293K Resolution 2.00 Å R-free 0.195

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TYB4_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain G; PDBConstruct 129–147; UniProt 28–46

Actin, alpha

OrganismNot specified

UniProt P02568

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 8–377 Not recorded Chimera of Gelsolin domain 1 and C-Terminal domain of thymosin Beta-4 × 1 (P06396,P20065) CA CALCIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 6.5;293 K;PEG 8000, Sodium acetate, calcium chloride, pH 6.5, microbatch, temperature 293K Resolution 2.00 Å R-free 0.195

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 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACTS_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–370; UniProt 8–377

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 1t44

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1t44
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1t44
Deposition date deposition_date2004-04-28
Structure title titleStructural basis of actin sequestration by thymosin-B4: Implications for arp2/3 activation
Keywords keywordsSTRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.15
Radius of gyration Rg (electron density) rg_electron24.33
Forward intensity I(0) i053630200.00
Molecular weight molecular_weight56843.0 kDa
Excluded volume excluded_volume71031 ų
Envelope volume envelope_volume83759 ų
Hydration-shell volume shell_volume28616 ų
Envelope diameter envelope_diameter90.0
Shell Rg shell_rg31.80
Envelope Rg envelope_rg24.70
Shape Rg shape_rg24.35
Total Rg total_rg25.08
Total atoms total_atoms3993
Residues n_residues502
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 dmax84.9
Rg (real space) rg_real25.12
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real5.3630e+07
I(0) uncertainty (real space) i0_real_error6.2470e+05
Rg (reciprocal space) rg_reciprocal25.13
I(0) (reciprocal space) i0_reciprocal53630000.0000
Solution quality estimate total_estimate0.8795
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.6
Skewness Skewness skewness0.342
Kurtosis Kurtosis kurtosis-0.259
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15470000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.971

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1t44a1
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_idd1t44a2
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_idd1t44g_
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 (5 domains)

Domain ID domain_id1t44A01
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_id1t44A02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology36 — Actin; Chain A, domain 2
Homologous superfamily homologous superfamily70 — Actin; Chain A, domain 2
Domain ID domain_id1t44A03
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_id1t44A04
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_id1t44G00
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)