3t5v

Sac3:Thp1:Sem1 complex

Method: X-RAY DIFFRACTION Dmax: 154.3 Å Quality: GOOD

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

Nuclear mRNA export protein SAC3

Saccharomyces cerevisiae

UniProt P46674

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 250–563 Fragment:M region, UNP 250-563 Nuclear mRNA export protein THP1 × 1 (Q08231) 26S proteasome complex subunit SEM1 × 1 (O94742) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.2;292 K;see publication, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 2.90 Å R-free 0.231
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 250–563 Fragment:M region, UNP 250-563 Nuclear mRNA export protein THP1 × 1 (Q08231) 26S proteasome complex subunit SEM1 × 1 (O94742) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.2;292 K;see publication, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 2.90 Å R-free 0.231

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.

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SAC3_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–316; UniProt 250–563 Author chain D; PDBConstruct 3–316; UniProt 250–563

Nuclear mRNA export protein THP1

Saccharomyces cerevisiae

UniProt Q08231

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 B; UniProt 1–455 Not recorded Nuclear mRNA export protein SAC3 × 1 (P46674) 26S proteasome complex subunit SEM1 × 1 (O94742) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.2;292 K;see publication, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 2.90 Å R-free 0.231
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 1–455 Not recorded Nuclear mRNA export protein SAC3 × 1 (P46674) 26S proteasome complex subunit SEM1 × 1 (O94742) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.2;292 K;see publication, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 2.90 Å R-free 0.231

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.

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

View Construct and Data Evidence
UniProt name THP1_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–455; UniProt 1–455 Author chain E; PDBConstruct 1–455; UniProt 1–455

26S proteasome complex subunit SEM1

Saccharomyces cerevisiae

UniProt O94742

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 1–89 Not recorded Nuclear mRNA export protein SAC3 × 1 (P46674) Nuclear mRNA export protein THP1 × 1 (Q08231) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.2;292 K;see publication, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 2.90 Å R-free 0.231
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 1–89 Not recorded Nuclear mRNA export protein SAC3 × 1 (P46674) Nuclear mRNA export protein THP1 × 1 (Q08231) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.2;292 K;see publication, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 2.90 Å R-free 0.231

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.

35 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SEM1_YEAST
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–89; UniProt 1–89 Author chain F; PDBConstruct 1–89; UniProt 1–89

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 3t5v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3t5v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3t5v
Deposition date deposition_date2011-07-28
Structure title titleSac3:Thp1:Sem1 complex
Keywords keywordsPCI, mRNA nuclear export, mRNA, nuclear, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier44.55
Radius of gyration Rg (electron density) rg_electron45.08
Forward intensity I(0) i0493273000.00
Molecular weight molecular_weight186810.0 kDa
Excluded volume excluded_volume235500 ų
Envelope volume envelope_volume310650 ų
Hydration-shell volume shell_volume61129 ų
Envelope diameter envelope_diameter161.9
Shell Rg shell_rg45.63
Envelope Rg envelope_rg44.90
Shape Rg shape_rg45.04
Total Rg total_rg45.25
Total atoms total_atoms26347
Residues n_residues1599
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 dmax154.3
Rg (real space) rg_real44.96
Rg uncertainty (real space) rg_real_error1.49
I(0) (real space) i0_real4.9330e+08
I(0) uncertainty (real space) i0_real_error9.3280e+06
Rg (reciprocal space) rg_reciprocal44.56
I(0) (reciprocal space) i0_reciprocal493000000.0000
Solution quality estimate total_estimate0.8096
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.1
Skewness Skewness skewness0.568
Kurtosis Kurtosis kurtosis-0.306
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha66720000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.706; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.803; Smooth: 0.598

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id3t5vA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily990
Domain ID domain_id3t5vD00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily990
Domain ID domain_id3t5vF01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1210

8. Citations (1)

9. Files and Curves (10)