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5suq

Crystal structure of the THO-Sub2 complex

Method: X-RAY DIFFRACTION Dmax: 269.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP-dependent RNA helicase SUB2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q07478

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–446 Chain C； UniProt 1–446 Not recorded Tex1 × 2 Tho2, Hpr1, Mft1, and Thp2 × 2 KEG 12-TUNGSTOPHOSPHATE × 11 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8.4；289 K；100 mM Tris-HCl (pH 8.4), 17.5% PEG3350, 2% methanol, 0.3 M NDSB-195 Resolution 6.00 Å R-free 0.434

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 5SUQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5SUP Crystal structure of the Sub2-Yra1 complex in association with RNA Deposited 2016-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric
Chain A 61–446（386 aa） Fragment：residues 61-446
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；277 K；100 mM Bis-Tris (pH 5.5), 20% PEG3350, 0.2 M ammonium acetate
Resolution 2.60 Å R-free 0.268
5SUP Crystal structure of the Sub2-Yra1 complex in association with RNA Deposited 2016-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric
Chain B 61–446（386 aa） Fragment：residues 61-446
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；277 K；100 mM Bis-Tris (pH 5.5), 20% PEG3350, 0.2 M ammonium acetate
Resolution 2.60 Å R-free 0.268
5SUP Crystal structure of the Sub2-Yra1 complex in association with RNA Deposited 2016-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric
Chain C 61–446（386 aa） Fragment：residues 61-446
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；277 K；100 mM Bis-Tris (pH 5.5), 20% PEG3350, 0.2 M ammonium acetate
Resolution 2.60 Å R-free 0.268
7APX yeast THO-Sub2 complex Deposited 2020-10-20 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 48–446（399 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
7LUV Cryo-EM structure of the yeast THO-Sub2 complex Deposited 2021-02-23 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain M 1–446（446 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7V2Y cryo-EM structure of yeast THO complex with Sub2 Deposited 2021-08-10 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 1–446（446 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8U8C Crystal structure of the TREX-2 complex in complex with the N-terminal motif of Sub2 Deposited 2023-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–55（55 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES, pH 6.5, and 20% PEG3350
Resolution 2.40 Å R-free 0.231

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SUB2_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–446； UniProt 1–446 Author chain C； PDBConstruct 1–446； UniProt 1–446

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 5suq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5suq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5suq
Deposition date deposition_date2016-08-03
Structure title titleCrystal structure of the THO-Sub2 complex
Keywords keywordsmRNA export, HYDROLASE; HYDROLASE
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_guinier72.95 Å
Radius of gyration Rg (electron density) rg_electron73.48 Å
Forward intensity I(0) i04676800000.00
Molecular weight molecular_weight456040.0 kDa
Excluded volume excluded_volume512050 ų
Envelope volume envelope_volume1439600 ų
Hydration-shell volume shell_volume165530 ų
Envelope diameter envelope_diameter261.5 Å
Shell Rg shell_rg70.98 Å
Envelope Rg envelope_rg72.59 Å
Shape Rg shape_rg74.21 Å
Total Rg total_rg71.58 Å
Total atoms total_atoms30788
Residues n_residues5585
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 dmax269.0 Å
Rg (real space) rg_real77.08 Å
Rg uncertainty (real space) rg_real_error1.77 Å
I(0) (real space) i0_real4.7130e+09
I(0) uncertainty (real space) i0_real_error1.0220e+08
Rg (reciprocal space) rg_reciprocal72.73 Å
I(0) (reciprocal space) i0_reciprocal4674000000.0000
Solution quality estimate total_estimate0.8636
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary89.7 Å
Skewness Skewness skewness0.627
Kurtosis Kurtosis kurtosis0.272
Angular range angular_range— – 0.1050 Å−1
Current regularization parameter α current_alpha0.9398
Highest regularization parameter α highest_alpha397700000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.721; Stabil: 0.858; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.540
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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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8. Citations (1)

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9. Files and Curves (10)