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7ntm

Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state

Method: ELECTRON MICROSCOPY Dmax: 104.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alcohol dehydrogenase 1

OrganismNot specified

UniProt P00330

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 2–348 Chain B； UniProt 2–348 Chain C； UniProt 2–348 Chain D； UniProt 2–348 Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.86 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 7NTM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4W6Z YEAST ALCOHOL DEHYDROGENASE I, SACCHAROMYCES CEREVISIAE FERMENTATIVE ENZYME Deposited 2014-08-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–348（347 aa）
Chain B 2–348（347 aa）
Not recorded ZN ZINC ION × 8 8ID NICOTINAMIDE-8-IODO-ADENINE-DINUCLEOTIDE × 2 ETF TRIFLUOROETHANOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；278 K；125 MM SODIUM N-TRIS(HYDROXYMETHYL) METHYL-3-AMINOPROPANE SULFONIC ACID, 1.7 MM NICOTINAMIDE 8- IODOADENINE DINUCLEOTIDE, 0.1 M 2,2,2-TRIFLUOROETHANOL, 0.16 MM EDTA, 10 MG/ML PROTEIN, 6% INITIAL POLYETHYLENE GLYCOL 5000 MONOMETHYL ETHER (FLUKA MPEG5000) IN DROP HANGING OVER 22-26% MPEG5000 AND 0.1 M 2,2,2-TRIFLUOROETHANOL. CRYSTALS WERE SOAKED IN SAME BUFFER WITH 30% W/V MPEG5000 WITH 0.5 M 2,2,2- TRIFLUOROETHANOL FOR FIVE DAYS BEFORE FREEZING AT 100 K., PH 8.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K, PH 8.40
Resolution 2.40 Å R-free 0.222
4W6Z YEAST ALCOHOL DEHYDROGENASE I, SACCHAROMYCES CEREVISIAE FERMENTATIVE ENZYME Deposited 2014-08-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain C 2–348（347 aa）
Chain D 2–348（347 aa）
Not recorded ZN ZINC ION × 8 8ID NICOTINAMIDE-8-IODO-ADENINE-DINUCLEOTIDE × 2 ETF TRIFLUOROETHANOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；278 K；125 MM SODIUM N-TRIS(HYDROXYMETHYL) METHYL-3-AMINOPROPANE SULFONIC ACID, 1.7 MM NICOTINAMIDE 8- IODOADENINE DINUCLEOTIDE, 0.1 M 2,2,2-TRIFLUOROETHANOL, 0.16 MM EDTA, 10 MG/ML PROTEIN, 6% INITIAL POLYETHYLENE GLYCOL 5000 MONOMETHYL ETHER (FLUKA MPEG5000) IN DROP HANGING OVER 22-26% MPEG5000 AND 0.1 M 2,2,2-TRIFLUOROETHANOL. CRYSTALS WERE SOAKED IN SAME BUFFER WITH 30% W/V MPEG5000 WITH 0.5 M 2,2,2- TRIFLUOROETHANOL FOR FIVE DAYS BEFORE FREEZING AT 100 K., PH 8.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K, PH 8.40
Resolution 2.40 Å R-free 0.222
5ENV YEAST ALCOHOL DEHYDROGENASE WITH BOUND COENZYME Deposited 2015-11-09 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–348（347 aa）
Chain B 2–348（347 aa）
Not recorded ZN ZINC ION × 8 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ETF TRIFLUOROETHANOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；298 K；100 MM SODIUM N-TRIS(HYDROXYMETHYL)METHYL-3-AMINOPROPANESULFONATE, 0.25 MM EDTA, 2 MM NAD+, 0.2 M 2,2,2-TRIFLUOROETHANOL, 1 MM YBCL3, 16 % POLYETHYETHYLENE GLYCOL 5000 MONOMETHYL ETHER, PH 8.4
Resolution 3.00 Å R-free 0.197

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

View Construct and Data Evidence
UniProt name ADH1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–347； UniProt 2–348 Author chain B； PDBConstruct 1–347； UniProt 2–348 Author chain C； PDBConstruct 1–347； UniProt 2–348 Author chain D； PDBConstruct 1–347； UniProt 2–348

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 7ntm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7ntm
Deposition date deposition_date2021-03-10
Structure title titleCryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state
Keywords keywordsADH1, tetramer, S.cerevisiae, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.99 Å
Radius of gyration Rg (electron density) rg_electron33.66 Å
Forward intensity I(0) i0333273000.00
Molecular weight molecular_weight147380.0 kDa
Excluded volume excluded_volume184540 ų
Envelope volume envelope_volume237110 ų
Hydration-shell volume shell_volume57018 ų
Envelope diameter envelope_diameter111.5 Å
Shell Rg shell_rg41.74 Å
Envelope Rg envelope_rg33.37 Å
Shape Rg shape_rg33.69 Å
Total Rg total_rg34.12 Å
Total atoms total_atoms10336
Residues n_residues1388
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 dmax104.4 Å
Rg (real space) rg_real33.82 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real3.3330e+08
I(0) uncertainty (real space) i0_real_error4.9790e+06
Rg (reciprocal space) rg_reciprocal33.93 Å
I(0) (reciprocal space) i0_reciprocal333300000.0000
Solution quality estimate total_estimate0.6888
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.4 Å
Skewness Skewness skewness0.139
Kurtosis Kurtosis kurtosis-0.493
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha73620000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 0.078; Positv: 1.000; Valcen: 0.987; Smooth: 0.921
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)