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1yrn

CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2 HOMEODOMAIN HETERODIMER BOUND TO DNA

Method: X-RAY DIFFRACTION Dmax: 69.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (MAT A1 HOMEODOMAIN)

Saccharomyces cerevisiae

UniProt P01366

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 Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain A； UniProt 66–126 Not recorded ;DNA (5'-D(*TP*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*C P*AP*TP*CP*A)-3') ; × 1 ;DNA (5'-D(*TP*AP*TP*GP*AP*TP*GP*TP*AP*AP*TP*AP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3') ; × 1 PROTEIN (MAT ALPHA2 HOMEODOMAIN) × 1 （Q6B2C0） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.50 Å R-free 0.298

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 1YRN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AKH MAT A1/ALPHA2/DNA TERNARY COMPLEX Deposited 1997-05-19 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 66–126（61 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；100MM HEPES PH 7.0, 20MM CACL2, 5MM [CO(NH3)6]CL3., VAPOR DIFFUSION, HANGING DROP, temperature 295.00K
Resolution 2.50 Å R-free 0.302
1F43 SOLUTION STRUCTURE OF THE MATA1 HOMEODOMAIN Deposited 2000-06-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 66–126（61 aa） Fragment：HOMEODOMAIN, C-TERMINAL DOMAIN (66-126)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure ambient
NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure ambient
NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure ambient
NMR sample composition 1.5 mM MATa1(66-126) U-15N,13C 25 mM deuterated acetate, pH 4.5, 100 mM KCl, 0.01% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.5 mM MATa1 (66-126) U-15N 25 mM deuterated acetate, pH 4.5, 100 mM KCl, 0.01% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.5 mM MATa1 (66-126) 25 mM deuterated acetate, pH 4.5, 100 mM KCl, 0.01% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
1LE8 Crystal Structure of the MATa1/MATalpha2-3A Heterodimer Bound to DNA Complex Deposited 2002-04-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 74–126（53 aa） Fragment：residues 74-126
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10% PEG400, 8 mM Co(NH3)6Cl3, 10 mM CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.299
1MH3 maltose binding-a1 homeodomain protein chimera, crystal form I Deposited 2002-08-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 77–126（50 aa）
Mutation：E359A, K362A, D363A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；amonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.262
1MH4 maltose binding-a1 homeodomain protein chimera, crystal form II Deposited 2002-08-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 77–126（50 aa）
Mutation：E359A, K362A, D363A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.293

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

View Construct and Data Evidence
UniProt name MATA1_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–61； UniProt 66–126

PROTEIN (MAT ALPHA2 HOMEODOMAIN)

Saccharomyces cerevisiae

UniProt Q6B2C0

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 Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain B； UniProt 128–210 Not recorded ;DNA (5'-D(*TP*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*C P*AP*TP*CP*A)-3') ; × 1 ;DNA (5'-D(*TP*AP*TP*GP*AP*TP*GP*TP*AP*AP*TP*AP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3') ; × 1 PROTEIN (MAT A1 HOMEODOMAIN) × 1 （P01366） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.50 Å R-free 0.298

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 1YRN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AKH MAT A1/ALPHA2/DNA TERNARY COMPLEX Deposited 1997-05-19 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 128–210（83 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；100MM HEPES PH 7.0, 20MM CACL2, 5MM [CO(NH3)6]CL3., VAPOR DIFFUSION, HANGING DROP, temperature 295.00K
Resolution 2.50 Å R-free 0.302
1APL CRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SUGGESTS A GENERAL MODEL FOR HOMEODOMAIN-DNA INTERACTIONS Deposited 1993-10-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain C 128–210（83 aa）
Chain D 128–210（83 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.50, VAPOR DIFFUSION, HANGING DROP
Resolution 2.70 Å
1MNM YEAST MATALPHA2/MCM1/DNA TERNARY TRANSCRIPTION COMPLEX CRYSTAL STRUCTURE Deposited 1997-11-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain C 103–189（87 aa） Fragment：RESIDUES 113 - 189
Chain D 103–189（87 aa） Fragment：RESIDUES 113 - 189
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；pH 5.50
Resolution 2.25 Å R-free 0.285

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

View Construct and Data Evidence
UniProt name MTAL2_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B； PDBConstruct 1–83； UniProt 128–210

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 1yrn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1yrn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1yrn
Deposition date deposition_date1995-11-02
Structure title titleCRYSTAL STRUCTURE OF THE MATA1/MATALPHA2 HOMEODOMAIN HETERODIMER BOUND TO DNA
Keywords keywordsCOMPLEX, DNA-BINDING PROTEIN, DNA, DNA BINDING PROTEIN-DNA COMPLEX; DNA BINDING PROTEIN/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_guinier20.89 Å
Radius of gyration Rg (electron density) rg_electron20.18 Å
Forward intensity I(0) i020447000.00
Molecular weight molecular_weight26966.0 kDa
Excluded volume excluded_volume30391 ų
Envelope volume envelope_volume38697 ų
Hydration-shell volume shell_volume16641 ų
Envelope diameter envelope_diameter70.7 Å
Shell Rg shell_rg25.77 Å
Envelope Rg envelope_rg20.13 Å
Shape Rg shape_rg20.13 Å
Total Rg total_rg20.90 Å
Total atoms total_atoms1849
Residues n_residues169
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 dmax69.0 Å
Rg (real space) rg_real20.93 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real2.0450e+07
I(0) uncertainty (real space) i0_real_error2.8560e+05
Rg (reciprocal space) rg_reciprocal20.92 Å
I(0) (reciprocal space) i0_reciprocal20450000.0000
Solution quality estimate total_estimate0.8933
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.0 Å
Skewness Skewness skewness0.349
Kurtosis Kurtosis kurtosis-0.453
Angular range angular_range— – 0.3800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2263000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.986
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1yrna_
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.1 — Homeodomain-like
Family Family familya.4.1.1 — Homeodomain
Domain ID domain_idd1yrnb_
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.1 — Homeodomain-like
Family Family familya.4.1.1 — Homeodomain

CATH v4.4 (2 domains)

Domain ID domain_id1yrnA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id1yrnB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
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8. Citations (2)

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9. Files and Curves (10)