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7luv

Cryo-EM structure of the yeast THO-Sub2 complex

Method: ELECTRON MICROSCOPY Dmax: 191.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

THO complex subunit HPR1

Saccharomyces cerevisiae

UniProt P17629

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 1–603 Not recorded THO complex subunit THP2 × 1 （O13539） THO complex subunit 2 × 1 （P53552） THO complex subunit MFT1 × 1 （P33441） Tex1 × 1 ATP-dependent RNA helicase SUB2 × 1 （Q07478） ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.70 Å

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 7LUV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7APX yeast THO-Sub2 complex Deposited 2020-10-20 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–720（720 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
7AQO yeast THO-Sub2 complex dimer Deposited 2020-10-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–720（720 aa）
Chain H 1–720（720 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 4.50 Å
7V2W protomer structure from the dimer of yeast THO complex Deposited 2021-08-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 1–752（752 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7V2Y cryo-EM structure of yeast THO complex with Sub2 Deposited 2021-08-10 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–752（752 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

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

View Construct and Data Evidence
UniProt name HPR1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–603； UniProt 1–603

THO complex subunit THP2

Saccharomyces cerevisiae

UniProt O13539

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 B； UniProt 1–261 Not recorded THO complex subunit HPR1 × 1 （P17629） THO complex subunit 2 × 1 （P53552） THO complex subunit MFT1 × 1 （P33441） Tex1 × 1 ATP-dependent RNA helicase SUB2 × 1 （Q07478） ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.70 Å

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 7LUV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7APX yeast THO-Sub2 complex Deposited 2020-10-20 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–261（261 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
7V2W protomer structure from the dimer of yeast THO complex Deposited 2021-08-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain J 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7V2Y cryo-EM structure of yeast THO complex with Sub2 Deposited 2021-08-10 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–261（261 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

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

View Construct and Data Evidence
UniProt name THP2_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–261； UniProt 1–261

THO complex subunit 2

Saccharomyces cerevisiae

UniProt P53552

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 C； UniProt 1–1257 Not recorded THO complex subunit HPR1 × 1 （P17629） THO complex subunit THP2 × 1 （O13539） THO complex subunit MFT1 × 1 （P33441） Tex1 × 1 ATP-dependent RNA helicase SUB2 × 1 （Q07478） ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.70 Å

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 7LUV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7APX yeast THO-Sub2 complex Deposited 2020-10-20 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–1597（1597 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
7V2W protomer structure from the dimer of yeast THO complex Deposited 2021-08-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain G 1–1597（1597 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7V2Y cryo-EM structure of yeast THO complex with Sub2 Deposited 2021-08-10 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–1597（1597 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

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

View Construct and Data Evidence
UniProt name THO2_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 6–1262； UniProt 1–1257

THO complex subunit MFT1

Saccharomyces cerevisiae

UniProt P33441

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 D； UniProt 1–256 Not recorded THO complex subunit HPR1 × 1 （P17629） THO complex subunit THP2 × 1 （O13539） THO complex subunit 2 × 1 （P53552） Tex1 × 1 ATP-dependent RNA helicase SUB2 × 1 （Q07478） ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.70 Å

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 7LUV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7APX yeast THO-Sub2 complex Deposited 2020-10-20 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–392（392 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
7AQO yeast THO-Sub2 complex dimer Deposited 2020-10-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–392（392 aa）
Chain I 1–392（392 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 4.50 Å
7V2W protomer structure from the dimer of yeast THO complex Deposited 2021-08-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 1–392（392 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7V2Y cryo-EM structure of yeast THO complex with Sub2 Deposited 2021-08-10 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–392（392 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

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

View Construct and Data Evidence
UniProt name MFT1_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–256； UniProt 1–256

ATP-dependent RNA helicase SUB2

Saccharomyces cerevisiae

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 M； UniProt 1–446 Not recorded THO complex subunit HPR1 × 1 （P17629） THO complex subunit THP2 × 1 （O13539） THO complex subunit 2 × 1 （P53552） THO complex subunit MFT1 × 1 （P33441） Tex1 × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.70 Å

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 7LUV 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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
5SUQ Crystal structure of the THO-Sub2 complex Deposited 2016-08-03 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 A 1–446（446 aa）
Chain C 1–446（446 aa）
Not recorded 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
7APX yeast THO-Sub2 complex Deposited 2020-10-20 Different construct 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
7V2Y cryo-EM structure of yeast THO complex with Sub2 Deposited 2021-08-10 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 oligomeric state Different experimental method 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 6
Chains and sequence ranges Author chain M； 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 7luv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7luv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7luv
Deposition date deposition_date2021-02-23
Structure title titleCryo-EM structure of the yeast THO-Sub2 complex
Keywords keywordsnuclear mRNA export, DEAD-box ATPase, mRNP remodeling, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier57.22 Å
Radius of gyration Rg (electron density) rg_electron57.03 Å
Forward intensity I(0) i0963953000.00
Molecular weight molecular_weight266030.0 kDa
Excluded volume excluded_volume335690 ų
Envelope volume envelope_volume529050 ų
Hydration-shell volume shell_volume80117 ų
Envelope diameter envelope_diameter214.2 Å
Shell Rg shell_rg55.22 Å
Envelope Rg envelope_rg57.22 Å
Shape Rg shape_rg57.07 Å
Total Rg total_rg56.83 Å
Total atoms total_atoms18773
Residues n_residues2378
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 dmax191.8 Å
Rg (real space) rg_real57.68 Å
Rg uncertainty (real space) rg_real_error1.90 Å
I(0) (real space) i0_real9.6390e+08
I(0) uncertainty (real space) i0_real_error1.9170e+07
Rg (reciprocal space) rg_reciprocal56.82 Å
I(0) (reciprocal space) i0_reciprocal962700000.0000
Solution quality estimate total_estimate0.8230
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary56.8 Å
Skewness Skewness skewness0.518
Kurtosis Kurtosis kurtosis-0.313
Angular range angular_range— – 0.1350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha69560000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.223
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)