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3coq

Structural Basis for Dimerization in DNA Recognition by Gal4

Method: X-RAY DIFFRACTION Dmax: 83.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Regulatory protein GAL4

Saccharomyces cerevisiae

UniProt P04386

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain A； UniProt 8–96 Chain B； UniProt 8–96 Fragment：DNA binding domain with complete dimerization domain ;DNA (5'-D(*DAP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DAP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3') ; × 1 ;DNA (5'-D(*DTP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DTP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3') ; × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.5；298 K；40mM Mg(OAc)2, 25mM sodium phosphate, 5% PEG400, 5% MPD, pH 5.5, VAPOR DIFFUSION, temperature 298K Resolution 2.40 Å R-free 0.269

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 3COQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AW6 GAL4 (CD), NMR, 24 STRUCTURES Deposited 1997-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–43（43 aa） Fragment：DNA-BINDING DOMAIN
Not recorded CD CADMIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.2；298 K
Resolution not provided
1D66 DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX Deposited 1992-03-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–65（65 aa）
Chain B 1–65（65 aa）
Not recorded CD CADMIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；pH 6.80, VAPOR DIFFUSION, HANGING DROP
Resolution 2.70 Å
1HBW Solution nmr structure of the dimerization domain of the yeast transcriptional activator Gal4 (residues 50-106) Deposited 2001-04-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 50–106（57 aa） Fragment：DIMERIZATION DOMAIN RESIDUES 50-106
Chain B 50–106（57 aa） Fragment：DIMERIZATION DOMAIN RESIDUES 50-106
Mutation：YES Mutation：YES No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；308 K；Ionic strength (raw mmCIF value) 50 MM SODIUM PHOSPHATE
Resolution not provided
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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 854–874（21 aa） Fragment：S. cerevisiae Gal4p peptide; UNP residues 854-874
Chain F 854–874（21 aa） Fragment：S. cerevisiae Gal4p peptide; UNP residues 854-874
Not recorded 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
7UIK Mediator-PIC Early (Tail A + Upstream DNA & Activator) Deposited 2022-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain T 1–147（147 aa）
Chain U 1–147（147 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.70 Å
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
Chain GA 1–147（147 aa）
Chain GB 1–147（147 aa）
Not recorded ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GAL4_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–89； UniProt 8–96 Author chain B； PDBConstruct 1–89； UniProt 8–96

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 3coq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3coq
Deposition date deposition_date2008-03-29
Structure title titleStructural Basis for Dimerization in DNA Recognition by Gal4
Keywords keywords;helix bundle, Protein-DNA complex, zinc binuclear cluster, Activator, Carbohydrate metabolism, DNA-binding, Galactose metabolism, Metal-binding, Nucleus, Phosphoprotein, Transcription, Transcription regulation, Transcription-DNA COMPLEX ;; Transcription/DNA
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_guinier25.83 Å
Radius of gyration Rg (electron density) rg_electron26.04 Å
Forward intensity I(0) i029318700.00
Molecular weight molecular_weight33561.0 kDa
Excluded volume excluded_volume38565 ų
Envelope volume envelope_volume55071 ų
Hydration-shell volume shell_volume19212 ų
Envelope diameter envelope_diameter87.8 Å
Shell Rg shell_rg31.13 Å
Envelope Rg envelope_rg25.76 Å
Shape Rg shape_rg25.99 Å
Total Rg total_rg26.70 Å
Total atoms total_atoms2280
Residues n_residues218
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 dmax83.3 Å
Rg (real space) rg_real25.84 Å
Rg uncertainty (real space) rg_real_error0.70 Å
I(0) (real space) i0_real2.9320e+07
I(0) uncertainty (real space) i0_real_error4.6990e+05
Rg (reciprocal space) rg_reciprocal25.84 Å
I(0) (reciprocal space) i0_reciprocal29320000.0000
Solution quality estimate total_estimate0.8953
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.2 Å
Skewness Skewness skewness0.161
Kurtosis Kurtosis kurtosis-0.786
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1130000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.875; Smooth: 0.996
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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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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3coqa1
Class classg — Small proteins
Fold Fold foldg.38 — Zn2/Cys6 DNA-binding domain
Superfamily Superfamily superfamilyg.38.1 — Zn2/Cys6 DNA-binding domain
Family Family familyg.38.1.1 — Zn2/Cys6 DNA-binding domain
Domain ID domain_idd3coqa2
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.3 — Leucine zipper domain
Family Family familyh.1.3.1 — Leucine zipper domain
Domain ID domain_idd3coqb1
Class classg — Small proteins
Fold Fold foldg.38 — Zn2/Cys6 DNA-binding domain
Superfamily Superfamily superfamilyg.38.1 — Zn2/Cys6 DNA-binding domain
Family Family familyg.38.1.1 — Zn2/Cys6 DNA-binding domain
Domain ID domain_idd3coqb2
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.3 — Leucine zipper domain
Family Family familyh.1.3.1 — Leucine zipper domain

CATH v4.4 (2 domains)

Domain ID domain_id3coqA00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology240 — CD2-Gal4
Homologous superfamily homologous superfamily10 — Zn(2)-C6 fungal-type DNA-binding domain
Domain ID domain_id3coqB00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology240 — CD2-Gal4
Homologous superfamily homologous superfamily10 — Zn(2)-C6 fungal-type DNA-binding domain
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8. Citations (1)

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9. Files and Curves (10)