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1wjo

Solution structure of the forth CH domain from human plastin 3 T-isoform

Method: SOLUTION NMR Dmax: 40.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

T-plastin

Homo sapiens

UniProt P13797

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 517–627 Fragment：CH domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.16mM CH domain U-15N,13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O | 90% H2O/10% D2O Resolution not provided

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 1WJO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AOA N-TERMINAL ACTIN-CROSSLINKING DOMAIN FROM HUMAN FIMBRIN Deposited 1997-06-30 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 98–372（275 aa） Fragment：ABD1
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 8-20: PEG 8000, 20 MM CALCIUM ACETATE, 100MM SODIUM CACODYLATE, PH 6.5
Resolution 2.40 Å R-free 0.285
7R94 T-Plastin-F-actin complex Deposited 2021-06-28 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 × 8 PDB declaration: octameric
Chain F 1–630（630 aa）
Chain G 1–630（630 aa）
Chain H 1–630（630 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7SX8 T-Plastin-F-actin complex, parallel bundled state Deposited 2021-11-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–630（630 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.00 Å
7SX9 T-Plastin-F-actin complex, anti-parallel bundled state Deposited 2021-11-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–630（630 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.00 Å
7SXA T-Plastin-F-actin complex, pre-bundling intermediate state Deposited 2021-11-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–630（630 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.87 Å

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

View Construct and Data Evidence
UniProt name PLST_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–118； UniProt 517–627

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 1wjo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1wjo
Deposition date deposition_date2004-05-29
Structure title titleSolution structure of the forth CH domain from human plastin 3 T-isoform
Keywords keywordsCH domain, actin binding, plastin 3, structural genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.24 Å
Radius of gyration Rg (electron density) rg_electron14.54 Å
Forward intensity I(0) i01042430000.00
Molecular weight molecular_weight264500.0 kDa
Excluded volume excluded_volume328310 ų
Envelope volume envelope_volume45060 ų
Hydration-shell volume shell_volume19155 ų
Envelope diameter envelope_diameter67.8 Å
Shell Rg shell_rg26.75 Å
Envelope Rg envelope_rg21.38 Å
Shape Rg shape_rg14.53 Å
Total Rg total_rg14.84 Å
Total atoms total_atoms37180
Residues n_residues2480
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 dmax40.0 Å
Rg (real space) rg_real14.35 Å
Rg uncertainty (real space) rg_real_error0.05 Å
I(0) (real space) i0_real9.8960e+08
I(0) uncertainty (real space) i0_real_error8.6060e+06
Rg (reciprocal space) rg_reciprocal15.29 Å
I(0) (reciprocal space) i0_reciprocal1042000000.0000
Solution quality estimate total_estimate0.6782
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.5 Å
Skewness Skewness skewness0.190
Kurtosis Kurtosis kurtosis-0.249
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha3.7690
Highest regularization parameter α highest_alpha463200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.005; Oscil: 0.964; Stabil: 0.982; Sysdev: 0.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1wjoa1
Class classa — All alpha proteins
Fold Fold folda.40 — CH domain-like
Superfamily Superfamily superfamilya.40.1 — Calponin-homology domain, CH-domain
Family Family familya.40.1.1 — Calponin-homology domain, CH-domain
Domain ID domain_idd1wjoa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1wjoa3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1wjoA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily10 — Calponin-like domain
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8. Citations (1)

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9. Files and Curves (10)