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3v2u

Crystal structure of the yeast GAL regulon complex of the repressor, Gal80p, and the transducer, Gal3p, with galactose and ATP

Method: X-RAY DIFFRACTION Dmax: 131.7 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Galactose/lactose metabolism regulatory protein GAL80

Saccharomyces cerevisiae

UniProt P04387

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–435 Chain B； UniProt 1–435 Not recorded Protein GAL3 × 2 （P13045） GOL GLYCEROL × 2 MG MAGNESIUM ION × 2 GLA alpha-D-galactopyranose × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；290 K；10% PEG 3350, 0.1M di-sodium succinate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 2.10 Å R-free 0.197

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 3V2U Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3BTS Crystal structure of a ternary complex of the transcriptional repressor Gal80p (Gal80S0 [G301R]) and the acidic activation domain of Gal4p (aa 854-874) from Saccharomyces cerevisiae with NAD Deposited 2007-12-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–435（435 aa）
Chain B 1–435（435 aa）
Mutation：G301R Mutation：G301R NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；20% PEG 3350, 0.15M Sodium fluoride, followed by soaking in NAD to a final concentration of 5mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.70 Å R-free 0.232
3BTU Crystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S2) [E351K] Deposited 2007-12-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–435（435 aa）
Chain B 1–435（435 aa）
Mutation：E351K Mutation：E351K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；290 K；0.1M CAPS, 0.2M NaCl, 20% PEG 8000, 50mM DTT, 4% Gamma-butyrolactone, 0.2M Sodium formate, 9% Sucrose, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.85 Å R-free 0.278
3BTU Crystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S2) [E351K] Deposited 2007-12-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–435（435 aa）
Chain D 1–435（435 aa）
Mutation：E351K Mutation：E351K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；290 K；0.1M CAPS, 0.2M NaCl, 20% PEG 8000, 50mM DTT, 4% Gamma-butyrolactone, 0.2M Sodium formate, 9% Sucrose, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.85 Å R-free 0.278
3BTU Crystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S2) [E351K] Deposited 2007-12-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–435（435 aa）
Chain F 1–435（435 aa）
Mutation：E351K Mutation：E351K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；290 K；0.1M CAPS, 0.2M NaCl, 20% PEG 8000, 50mM DTT, 4% Gamma-butyrolactone, 0.2M Sodium formate, 9% Sucrose, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.85 Å R-free 0.278
3BTV Crystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S0)-[G301R] Deposited 2007-12-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–435（435 aa）
Chain B 1–435（435 aa）
Mutation：G301R Mutation：G301R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；20% PEG 3350, 0.15M Sodium Fluoride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å R-free 0.257

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

View Construct and Data Evidence
UniProt name GAL80_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–438； UniProt 1–435 Author chain B； PDBConstruct 4–438； UniProt 1–435

Protein GAL3

Saccharomyces cerevisiae

UniProt P13045

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 2–520 Chain D； UniProt 2–520 Not recorded Galactose/lactose metabolism regulatory protein GAL80 × 2 （P04387） GOL GLYCEROL × 2 MG MAGNESIUM ION × 2 GLA alpha-D-galactopyranose × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；290 K；10% PEG 3350, 0.1M di-sodium succinate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 2.10 Å R-free 0.197

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 3V2U Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3V5R Crystal structure of the unliganded form of Gal3p Deposited 2011-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 17–520（504 aa）
Chain B 17–520（504 aa）
Not recorded SO4 SULFATE ION × 27 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；290 K；10 mM MgCl2, 50 mM MES, 1.85M Li2SO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å R-free 0.202
3V5R Crystal structure of the unliganded form of Gal3p Deposited 2011-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 17–520（504 aa）
Chain B 17–520（504 aa）
Not recorded SO4 SULFATE ION × 54 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；290 K；10 mM MgCl2, 50 mM MES, 1.85M Li2SO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å R-free 0.202
3V5R Crystal structure of the unliganded form of Gal3p Deposited 2011-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 17–520（504 aa）
Chain B 17–520（504 aa）
Not recorded SO4 SULFATE ION × 54 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；290 K；10 mM MgCl2, 50 mM MES, 1.85M Li2SO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å R-free 0.202
3V5R Crystal structure of the unliganded form of Gal3p Deposited 2011-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 17–520（504 aa）
Chain B 17–520（504 aa）
Not recorded SO4 SULFATE ION × 54 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；290 K；10 mM MgCl2, 50 mM MES, 1.85M Li2SO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å R-free 0.202

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

View Construct and Data Evidence
UniProt name GAL3_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 2–520； UniProt 2–520 Author chain D； PDBConstruct 2–520； UniProt 2–520

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 3v2u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3v2u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3v2u
Deposition date deposition_date2011-12-12
Structure title titleCrystal structure of the yeast GAL regulon complex of the repressor, Gal80p, and the transducer, Gal3p, with galactose and ATP
Keywords keywordsRossmann fold, GHMP superfamily, Transcription regulation, TRANSCRIPTION; TRANSCRIPTION
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_guinier40.83 Å
Radius of gyration Rg (electron density) rg_electron40.51 Å
Forward intensity I(0) i0620455000.00
Molecular weight molecular_weight206830.0 kDa
Excluded volume excluded_volume259650 ų
Envelope volume envelope_volume334160 ų
Hydration-shell volume shell_volume67232 ų
Envelope diameter envelope_diameter130.8 Å
Shell Rg shell_rg47.26 Å
Envelope Rg envelope_rg40.12 Å
Shape Rg shape_rg40.51 Å
Total Rg total_rg40.85 Å
Total atoms total_atoms14565
Residues n_residues1841
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 dmax131.7 Å
Rg (real space) rg_real40.75 Å
Rg uncertainty (real space) rg_real_error1.12 Å
I(0) (real space) i0_real6.2050e+08
I(0) uncertainty (real space) i0_real_error1.0570e+07
Rg (reciprocal space) rg_reciprocal40.83 Å
I(0) (reciprocal space) i0_reciprocal620500000.0000
Solution quality estimate total_estimate0.9022
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.7 Å
Skewness Skewness skewness0.219
Kurtosis Kurtosis kurtosis-0.573
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha139700000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.934
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id3v2uA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3v2uA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id3v2uB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3v2uB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id3v2uC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3v2uC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily3170 —
Domain ID domain_id3v2uC03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily340 —
Domain ID domain_id3v2uD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3v2uD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily3170 —
Domain ID domain_id3v2uD03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily340 —
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8. Citations (1)

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9. Files and Curves (10)