3wut

Structure basis of inactivating cell abscission

Method: X-RAY DIFFRACTION Dmax: 98.8 Å Quality: EXCELLENT

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

Centrosomal protein of 55 kDa

Homo sapiens

UniProt Q53EZ4

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 160–217 Chain B; UniProt 160–217 Fragment:UNP residues 160-217 Inactive serine/threonine-protein kinase TEX14 × 1 (Q8IWB6) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;295 K;1M ammonium phosphate dibasic, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.30 Å R-free 0.259
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 160–217 Chain E; UniProt 160–217 Fragment:UNP residues 160-217 Inactive serine/threonine-protein kinase TEX14 × 1 (Q8IWB6) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;295 K;1M ammonium phosphate dibasic, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.30 Å R-free 0.259
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 160–217 Chain H; UniProt 160–217 Fragment:UNP residues 160-217 Inactive serine/threonine-protein kinase TEX14 × 1 (Q8IWB6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;295 K;1M ammonium phosphate dibasic, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.30 Å R-free 0.259
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain J; UniProt 160–217 Chain K; UniProt 160–217 Fragment:UNP residues 160-217 Inactive serine/threonine-protein kinase TEX14 × 1 (Q8IWB6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;295 K;1M ammonium phosphate dibasic, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.30 Å R-free 0.259

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.

3 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CEP55_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 6–63; UniProt 160–217 Author chain B; PDBConstruct 6–63; UniProt 160–217 Author chain D; PDBConstruct 6–63; UniProt 160–217 Author chain E; PDBConstruct 6–63; UniProt 160–217 Author chain G; PDBConstruct 6–63; UniProt 160–217 Author chain H; PDBConstruct 6–63; UniProt 160–217 Author chain J; PDBConstruct 6–63; UniProt 160–217 Author chain K; PDBConstruct 6–63; UniProt 160–217

Inactive serine/threonine-protein kinase TEX14

OrganismNot specified

UniProt Q8IWB6

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 792–804 Fragment:UNP residues 792-804 Centrosomal protein of 55 kDa × 2 (Q53EZ4) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;295 K;1M ammonium phosphate dibasic, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.30 Å R-free 0.259
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 792–804 Fragment:UNP residues 792-804 Centrosomal protein of 55 kDa × 2 (Q53EZ4) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;295 K;1M ammonium phosphate dibasic, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.30 Å R-free 0.259
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain I; UniProt 792–804 Fragment:UNP residues 792-804 Centrosomal protein of 55 kDa × 2 (Q53EZ4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;295 K;1M ammonium phosphate dibasic, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.30 Å R-free 0.259
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain L; UniProt 792–804 Fragment:UNP residues 792-804 Centrosomal protein of 55 kDa × 2 (Q53EZ4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;295 K;1M ammonium phosphate dibasic, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.30 Å R-free 0.259

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 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TEX14_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 2–14; UniProt 792–804 Author chain F; PDBConstruct 2–14; UniProt 792–804 Author chain I; PDBConstruct 2–14; UniProt 792–804 Author chain L; PDBConstruct 2–14; UniProt 792–804

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 3wut

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3wut
Deposition date deposition_date2014-05-05
Structure title titleStructure basis of inactivating cell abscission
Keywords keywordsCoiled-coil, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.39
Radius of gyration Rg (electron density) rg_electron29.54
Forward intensity I(0) i042341000.00
Molecular weight molecular_weight52696.0 kDa
Excluded volume excluded_volume66966 ų
Envelope volume envelope_volume91869 ų
Hydration-shell volume shell_volume27356 ų
Envelope diameter envelope_diameter104.0
Shell Rg shell_rg34.45
Envelope Rg envelope_rg30.26
Shape Rg shape_rg29.47
Total Rg total_rg30.32
Total atoms total_atoms3718
Residues n_residues447
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 dmax98.8
Rg (real space) rg_real30.35
Rg uncertainty (real space) rg_real_error0.89
I(0) (real space) i0_real4.2340e+07
I(0) uncertainty (real space) i0_real_error6.7950e+05
Rg (reciprocal space) rg_reciprocal30.37
I(0) (reciprocal space) i0_reciprocal42340000.0000
Solution quality estimate total_estimate0.9049
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.9
Skewness Skewness skewness0.183
Kurtosis Kurtosis kurtosis-0.523
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2465000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.942

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id3wutA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1180 — Geminin coiled-coil domain
Domain ID domain_id3wutB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1180 — Geminin coiled-coil domain
Domain ID domain_id3wutD00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1180 — Geminin coiled-coil domain
Domain ID domain_id3wutE00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1180 — Geminin coiled-coil domain
Domain ID domain_id3wutG00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1180 — Geminin coiled-coil domain
Domain ID domain_id3wutH00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1180 — Geminin coiled-coil domain
Domain ID domain_id3wutJ00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1180 — Geminin coiled-coil domain
Domain ID domain_id3wutK00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1180 — Geminin coiled-coil domain

8. Citations (1)

9. Files and Curves (10)