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3u9d

Crystal Structure of a chimera containing the N-terminal domain (residues 8-24) of drosophila Ciboulot and the C-terminal domain (residues 13-44) of bovine Thymosin-beta4, bound to G-actin-ATP

Method: X-RAY DIFFRACTION Dmax: 120.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin, alpha skeletal muscle

OrganismNot specified

UniProt P68136

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 3–377 Not recorded Thymosin beta-4, Chimeric protein × 1 （P62326,O97428） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 6.5；298 K；18% PEG3350, 0.05M NaAcetate pH4.7, 0.1M MgAcetate pH6.5, 0.32M Guanidine HCl, 0.8% Dioxane, hanging drop, temperature 298K Resolution 2.50 Å R-free 0.240
2 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 3–377 Not recorded Thymosin beta-4, Chimeric protein × 1 （P62326,O97428） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 6.5；298 K；18% PEG3350, 0.05M NaAcetate pH4.7, 0.1M MgAcetate pH6.5, 0.32M Guanidine HCl, 0.8% Dioxane, hanging drop, temperature 298K Resolution 2.50 Å R-free 0.240

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 3U9D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8ZBM RAT skeletal muscle ATM complex Deposited 2024-04-26 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 × 16 PDB declaration: 16-meric
Chain E 7–377（371 aa）
Chain H 7–377（371 aa）
Chain O 7–377（371 aa）
Chain P 7–377（371 aa）
Chain Q 7–377（371 aa）
Chain R 7–377（371 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8ZIX RAT skeletal muscle F-actin Deposited 2024-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 7–377（371 aa）
Chain B 7–377（371 aa）
Chain E 7–377（371 aa）
Chain F 7–377（371 aa）
Chain P 7–377（371 aa）
Chain R 7–377（371 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACTS_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–375； UniProt 3–377 Author chain C； PDBConstruct 1–375； UniProt 3–377

Thymosin beta-4, Chimeric protein

Bos taurus

UniProt O97428

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 B； UniProt 8–24 Fragment：UNP O97428 residues 8-24, UNP P62326 residues 13-44 Actin, alpha skeletal muscle × 1 （P68136） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 6.5；298 K；18% PEG3350, 0.05M NaAcetate pH4.7, 0.1M MgAcetate pH6.5, 0.32M Guanidine HCl, 0.8% Dioxane, hanging drop, temperature 298K Resolution 2.50 Å R-free 0.240
2 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 8–24 Fragment：UNP O97428 residues 8-24, UNP P62326 residues 13-44 Actin, alpha skeletal muscle × 1 （P68136） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 6.5；298 K；18% PEG3350, 0.05M NaAcetate pH4.7, 0.1M MgAcetate pH6.5, 0.32M Guanidine HCl, 0.8% Dioxane, hanging drop, temperature 298K Resolution 2.50 Å R-free 0.240

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 3U9D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1SQK CRYSTAL STRUCTURE OF CIBOULOT IN COMPLEX WITH SKELETAL ACTIN Deposited 2004-03-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–34（25 aa） Fragment：residues 10-34
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 LAR LATRUNCULIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；PEG 8000 20%, MAGNESIUM ACETATE 200MM, SODIUM CACODYLATE 100 MM, pH 6.50, VAPOR DIFFUSION, HANGING DROP
Resolution 2.50 Å R-free 0.278
3SJH Crystal Structure of a chimera containing the N-terminal domain (residues 8-29) of drosophila Ciboulot and the C-terminal domain (residues 18-44) of bovine Thymosin-beta4, bound to G-actin-ATP-Latrunculin A Deposited 2011-06-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 8–29（22 aa） Fragment：UNP O97428 residues 8-29, UNP P62326 residues 18-44
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 LAR LATRUNCULIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；298 K；22% PEG3350, 0.2M MgAcetate pH6.5, 0.45M Guanidine HCl, 1% Dioxane, hanging drop, temperature 298K
Resolution 1.75 Å R-free 0.199
3U8X Crystal Structure of a chimera containing the N-terminal domain (residues 8-29) of drosophila Ciboulot and the C-terminal domain (residues 18-44) of bovine Thymosin-beta4, bound to G-actin-ATP Deposited 2011-10-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 8–29（22 aa） Fragment：UNP O97428 residues 8-29, UNP P62326 residues 18-44
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；298 K；20% PEG3350, 0.2M MgAcetate pH6.5, 0.45M Guanidine HCl, 1% Dioxane, hanging drop, temperature 298K
Resolution 2.00 Å R-free 0.238
3U8X Crystal Structure of a chimera containing the N-terminal domain (residues 8-29) of drosophila Ciboulot and the C-terminal domain (residues 18-44) of bovine Thymosin-beta4, bound to G-actin-ATP Deposited 2011-10-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 8–29（22 aa） Fragment：UNP O97428 residues 8-29, UNP P62326 residues 18-44
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；298 K；20% PEG3350, 0.2M MgAcetate pH6.5, 0.45M Guanidine HCl, 1% Dioxane, hanging drop, temperature 298K
Resolution 2.00 Å R-free 0.238
3U9Z Crystal structure between actin and a protein construct containing the first beta-thymosin domain of drosophila ciboulot (residues 2-58) with the three mutations N26D/Q27K/D28S Deposited 2011-10-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–58（57 aa） Fragment：UNP residues 2-58
Mutation：N26D, Q27K, D28S ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；298 K；18% PEG3350, 0.05M NaAcetate pH4.7, 0.1M MgAcetate pH6.5, 0.32M Guanidine HCl, 0.8% Dioxane, hanging drop, temperature 298K
Resolution 2.09 Å R-free 0.227

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O97428_DROME
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 6–22； UniProt 8–24 Author chain D； PDBConstruct 6–22； UniProt 8–24

Thymosin beta-4, Chimeric protein

Bos taurus

UniProt P62326

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 B； UniProt 13–44 Fragment：UNP O97428 residues 8-24, UNP P62326 residues 13-44 Actin, alpha skeletal muscle × 1 （P68136） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 6.5；298 K；18% PEG3350, 0.05M NaAcetate pH4.7, 0.1M MgAcetate pH6.5, 0.32M Guanidine HCl, 0.8% Dioxane, hanging drop, temperature 298K Resolution 2.50 Å R-free 0.240
2 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 13–44 Fragment：UNP O97428 residues 8-24, UNP P62326 residues 13-44 Actin, alpha skeletal muscle × 1 （P68136） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 6.5；298 K；18% PEG3350, 0.05M NaAcetate pH4.7, 0.1M MgAcetate pH6.5, 0.32M Guanidine HCl, 0.8% Dioxane, hanging drop, temperature 298K Resolution 2.50 Å R-free 0.240

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 3U9D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3SJH Crystal Structure of a chimera containing the N-terminal domain (residues 8-29) of drosophila Ciboulot and the C-terminal domain (residues 18-44) of bovine Thymosin-beta4, bound to G-actin-ATP-Latrunculin A Deposited 2011-06-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 18–44（27 aa） Fragment：UNP O97428 residues 8-29, UNP P62326 residues 18-44
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 LAR LATRUNCULIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；298 K；22% PEG3350, 0.2M MgAcetate pH6.5, 0.45M Guanidine HCl, 1% Dioxane, hanging drop, temperature 298K
Resolution 1.75 Å R-free 0.199
3U8X Crystal Structure of a chimera containing the N-terminal domain (residues 8-29) of drosophila Ciboulot and the C-terminal domain (residues 18-44) of bovine Thymosin-beta4, bound to G-actin-ATP Deposited 2011-10-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 18–44（27 aa） Fragment：UNP O97428 residues 8-29, UNP P62326 residues 18-44
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；298 K；20% PEG3350, 0.2M MgAcetate pH6.5, 0.45M Guanidine HCl, 1% Dioxane, hanging drop, temperature 298K
Resolution 2.00 Å R-free 0.238
3U8X Crystal Structure of a chimera containing the N-terminal domain (residues 8-29) of drosophila Ciboulot and the C-terminal domain (residues 18-44) of bovine Thymosin-beta4, bound to G-actin-ATP Deposited 2011-10-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 18–44（27 aa） Fragment：UNP O97428 residues 8-29, UNP P62326 residues 18-44
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；298 K；20% PEG3350, 0.2M MgAcetate pH6.5, 0.45M Guanidine HCl, 1% Dioxane, hanging drop, temperature 298K
Resolution 2.00 Å R-free 0.238

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TYB4_BOVIN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 23–54； UniProt 13–44 Author chain D； PDBConstruct 23–54； UniProt 13–44

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 3u9d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3u9d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3u9d
Deposition date deposition_date2011-10-18
Structure title titleCrystal Structure of a chimera containing the N-terminal domain (residues 8-24) of drosophila Ciboulot and the C-terminal domain (residues 13-44) of bovine Thymosin-beta4, bound to G-actin-ATP
Keywords keywordsCONTRACTILE PROTEIN, PROTEIN BINDING; CONTRACTILE PROTEIN, PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.46 Å
Radius of gyration Rg (electron density) rg_electron35.57 Å
Forward intensity I(0) i0115052000.00
Molecular weight molecular_weight85361.0 kDa
Excluded volume excluded_volume106540 ų
Envelope volume envelope_volume138030 ų
Hydration-shell volume shell_volume34597 ų
Envelope diameter envelope_diameter128.7 Å
Shell Rg shell_rg38.97 Å
Envelope Rg envelope_rg35.37 Å
Shape Rg shape_rg35.53 Å
Total Rg total_rg35.94 Å
Total atoms total_atoms5986
Residues n_residues756
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax120.2 Å
Rg (real space) rg_real35.80 Å
Rg uncertainty (real space) rg_real_error1.30 Å
I(0) (real space) i0_real1.1510e+08
I(0) uncertainty (real space) i0_real_error2.0690e+06
Rg (reciprocal space) rg_reciprocal35.59 Å
I(0) (reciprocal space) i0_reciprocal115000000.0000
Solution quality estimate total_estimate0.8137
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.4 Å
Skewness Skewness skewness0.503
Kurtosis Kurtosis kurtosis-0.526
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30330000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.698; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.676; Smooth: 0.804
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3u9da1
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_idd3u9da2
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_idd3u9dc1
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_idd3u9dc2
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

CATH v4.4 (6 domains)

Domain ID domain_id3u9dA01
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_id3u9dA02
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_id3u9dA03
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_id3u9dC01
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_id3u9dC02
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_id3u9dC03
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
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8. Citations (2)

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9. Files and Curves (10)