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- EMDB-12591: Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-12591
TitleCryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state
Map dataLocal sharpen cryo-EM map of apo ADH1
Sample
  • Complex: Tetrameric structure of native ADH1 from S. cereviciae in its apo state.
    • Protein or peptide: Alcohol dehydrogenase 1
  • Ligand: ZINC ION
KeywordsADH1 / tetramer / S.cerevisiae / OXIDOREDUCTASE
Function / homology
Function and homology information


methylglyoxal reductase (NADH) / octanol dehydrogenase (NAD+) activity / methylglyoxal reductase (NADH) activity / pyruvate fermentation to ethanol / amino acid catabolic process to alcohol via Ehrlich pathway / butanol dehydrogenase (NAD+) activity / ethanol dehydrogenase (NAD+) activity / melatonin binding / alcohol dehydrogenase (NAD+) activity / allyl-alcohol dehydrogenase ...methylglyoxal reductase (NADH) / octanol dehydrogenase (NAD+) activity / methylglyoxal reductase (NADH) activity / pyruvate fermentation to ethanol / amino acid catabolic process to alcohol via Ehrlich pathway / butanol dehydrogenase (NAD+) activity / ethanol dehydrogenase (NAD+) activity / melatonin binding / alcohol dehydrogenase (NAD+) activity / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / alcohol dehydrogenase / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Alcohol dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsNzigou Mandouckou JA / Carroni M
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council2018-02818 Sweden
CitationJournal: To Be Published
Title: Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state
Authors: Nzigou Mandouckou JA / Carroni M / Haeggstrom JZ / Thulasingam M
History
DepositionMar 10, 2021-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_12591.png

Downloads & links

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Map

FileDownload / File: emd_12591.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal sharpen cryo-EM map of apo ADH1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.61 Å/pix.
x 400 pix.
= 242.88 Å		0.61 Å/pix.
x 400 pix.
= 242.88 Å		0.61 Å/pix.
x 400 pix.
= 242.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.185
Minimum - Maximum-0.044863712 - 0.54785806
Average (Standard dev.)-0.000000000002401 (±0.022352392)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 242.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_12591_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unfiltered cryo-EM map of apo ADH1

Fileemd_12591_additional_1.map
AnnotationUnfiltered cryo-EM map of apo ADH1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of cryo-EM map of apo ADH1

Fileemd_12591_half_map_1.map
AnnotationHalf map A of cryo-EM map of apo ADH1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of cryo-EM map of apo ADH1

Fileemd_12591_half_map_2.map
AnnotationHalf map B of cryo-EM map of apo ADH1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrameric structure of native ADH1 from S. cereviciae in its apo...

EntireName: Tetrameric structure of native ADH1 from S. cereviciae in its apo state.
Components
  • Complex: Tetrameric structure of native ADH1 from S. cereviciae in its apo state.
    • Protein or peptide: Alcohol dehydrogenase 1
  • Ligand: ZINC ION

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Supramolecule #1: Tetrameric structure of native ADH1 from S. cereviciae in its apo...

SupramoleculeName: Tetrameric structure of native ADH1 from S. cereviciae in its apo state.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Stable homotetramer, composed of four monomers labelled as A, B, C and D.
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 147 KDa

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Macromolecule #1: Alcohol dehydrogenase 1

MacromoleculeName: Alcohol dehydrogenase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: alcohol dehydrogenase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 36.759906 KDa
SequenceString: SIPETQKGVI FYESHGKLEY KDIPVPKPKA NELLINVKYS GVCHTDLHAW HGDWPLPVKL PLVGGHEGAG VVVGMGENVK GWKIGDYAG IKWLNGSCMA CEYCELGNES NCPHADLSGY THDGSFQQYA TADAVQAAHI PQGTDLAQVA PILCAGITVY K ALKSANLM ...String:
SIPETQKGVI FYESHGKLEY KDIPVPKPKA NELLINVKYS GVCHTDLHAW HGDWPLPVKL PLVGGHEGAG VVVGMGENVK GWKIGDYAG IKWLNGSCMA CEYCELGNES NCPHADLSGY THDGSFQQYA TADAVQAAHI PQGTDLAQVA PILCAGITVY K ALKSANLM AGHWVAISGA AGGLGSLAVQ YAKAMGYRVL GIDGGEGKEE LFRSIGGEVF IDFTKEKDIV GAVLKATDGG AH GVINVSV SEAAIEASTR YVRANGTTVL VGMPAGAKCC SDVFNQVVKS ISIVGSYVGN RADTREALDF FARGLVKSPI KVV GLSTLP EIYEKMEKGQ IVGRYVVDTS K

UniProtKB: Alcohol dehydrogenase 1

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureComa free - Residual tilt: 130.0 mrad
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 14964 / Average exposure time: 2.5 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 639189
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5env

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2.15.041) / Number images used: 222802
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. v2.15.041) / Details: SGD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v2.15.041)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5env


Chain - Chain ID: A / Chain - Residue range: 1-347 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsModel building and refinement were done using using CCP-EM software suite (Burnley et al, 2017). The X-ray structure of yeast ADH1 (PDB: 5ENV) was used as a starting model for model building. This model was docked into our Cryo-EM map using MolRep (Brown et al, 2014). The resulting starting model was manually adjusted in Coot (Emsley et al, 2010). REFMAC 5 (Brown et al, 2014) used for structure model refinement.
RefinementSpace: REAL / Protocol: BACKBONE TRACE / Overall B value: 123
Output model

PDB-7ntm:
Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state

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