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7v2y

cryo-EM structure of yeast THO complex with Sub2

Method: ELECTRON MICROSCOPY Dmax: 199.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

THO complex subunit HPR1

Saccharomyces cerevisiae S288c

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 1–752 Not recorded THO complex subunit 2 × 1 （P53552） Protein TEX1 × 1 （P53851） THO complex subunit MFT1 × 1 （P33441） THO complex subunit THP2 × 1 （O13539） ATP-dependent RNA helicase SUB2 × 1 （Q07478） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.40 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 7V2Y 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 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
7LUV Cryo-EM structure of the yeast THO-Sub2 complex Deposited 2021-02-23 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–603（603 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
7V2W protomer structure from the dimer of yeast THO complex Deposited 2021-08-10 Different oligomeric state 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

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 1–752； UniProt 1–752

THO complex subunit 2

Saccharomyces cerevisiae S288c

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 B； UniProt 1–1597 Not recorded THO complex subunit HPR1 × 1 （P17629） Protein TEX1 × 1 （P53851） THO complex subunit MFT1 × 1 （P33441） THO complex subunit THP2 × 1 （O13539） ATP-dependent RNA helicase SUB2 × 1 （Q07478） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.40 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 7V2Y 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 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
7LUV Cryo-EM structure of the yeast THO-Sub2 complex Deposited 2021-02-23 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1257（1257 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
7V2W protomer structure from the dimer of yeast THO complex Deposited 2021-08-10 Different oligomeric state 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

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 2
Chains and sequence ranges Author chain B； PDBConstruct 1–1597； UniProt 1–1597

Protein TEX1

Saccharomyces cerevisiae S288c

UniProt P53851

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 1–422 Not recorded THO complex subunit HPR1 × 1 （P17629） THO complex subunit 2 × 1 （P53552） THO complex subunit MFT1 × 1 （P33441） THO complex subunit THP2 × 1 （O13539） ATP-dependent RNA helicase SUB2 × 1 （Q07478） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.40 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 7V2Y 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–380（380 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 1–422（422 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

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TEX1_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–422； UniProt 1–422

THO complex subunit MFT1

Saccharomyces cerevisiae S288c

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 1–392 Not recorded THO complex subunit HPR1 × 1 （P17629） THO complex subunit 2 × 1 （P53552） Protein TEX1 × 1 （P53851） THO complex subunit THP2 × 1 （O13539） ATP-dependent RNA helicase SUB2 × 1 （Q07478） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.40 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 7V2Y 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 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
7LUV Cryo-EM structure of the yeast THO-Sub2 complex Deposited 2021-02-23 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–256（256 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
7V2W protomer structure from the dimer of yeast THO complex Deposited 2021-08-10 Different oligomeric state 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

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 1–392； UniProt 1–392

THO complex subunit THP2

Saccharomyces cerevisiae S288c

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 E； UniProt 1–261 Not recorded THO complex subunit HPR1 × 1 （P17629） THO complex subunit 2 × 1 （P53552） Protein TEX1 × 1 （P53851） THO complex subunit MFT1 × 1 （P33441） ATP-dependent RNA helicase SUB2 × 1 （Q07478） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.40 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 7V2Y 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 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
7LUV Cryo-EM structure of the yeast THO-Sub2 complex Deposited 2021-02-23 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–261（261 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
7V2W protomer structure from the dimer of yeast THO complex Deposited 2021-08-10 Different oligomeric state 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

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 5
Chains and sequence ranges Author chain E； PDBConstruct 1–261； UniProt 1–261

ATP-dependent RNA helicase SUB2

Saccharomyces cerevisiae 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 F； UniProt 1–446 Not recorded THO complex subunit HPR1 × 1 （P17629） THO complex subunit 2 × 1 （P53552） Protein TEX1 × 1 （P53851） THO complex subunit MFT1 × 1 （P33441） THO complex subunit THP2 × 1 （O13539） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.40 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 7V2Y 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 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 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
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 F； 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 7v2y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7v2y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7v2y
Deposition date deposition_date2021-08-10
Structure title titlecryo-EM structure of yeast THO complex with Sub2
Keywords keywordsRNA transcription, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier61.93 Å
Radius of gyration Rg (electron density) rg_electron62.34 Å
Forward intensity I(0) i01462580000.00
Molecular weight molecular_weight327870.0 kDa
Excluded volume excluded_volume413290 ų
Envelope volume envelope_volume646860 ų
Hydration-shell volume shell_volume90548 ų
Envelope diameter envelope_diameter225.2 Å
Shell Rg shell_rg58.18 Å
Envelope Rg envelope_rg62.22 Å
Shape Rg shape_rg62.32 Å
Total Rg total_rg62.34 Å
Total atoms total_atoms23097
Residues n_residues2846
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 dmax199.8 Å
Rg (real space) rg_real62.61 Å
Rg uncertainty (real space) rg_real_error2.05 Å
I(0) (real space) i0_real1.4620e+09
I(0) uncertainty (real space) i0_real_error3.1290e+07
Rg (reciprocal space) rg_reciprocal61.25 Å
I(0) (reciprocal space) i0_reciprocal1459000000.0000
Solution quality estimate total_estimate0.8034
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary55.9 Å
Skewness Skewness skewness0.536
Kurtosis Kurtosis kurtosis-0.437
Angular range angular_range— – 0.1250 Å−1
Current regularization parameter α current_alpha0.0006
Highest regularization parameter α highest_alpha108600000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.808; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.057
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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)