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- EMDB-50545: Alcohol dehydrogenase -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50545
TitleAlcohol dehydrogenase
Map dataRelion blush map
Sample
  • Complex: PDEN_2367
    • Protein or peptide: alcohol dehydrogenase
  • Ligand: ZINC ION
  • Ligand: water
KeywordsAlcohol dehydrogenase / tetramer / OXIDOREDUCTASE
Function / homology
Function and homology information


alcohol dehydrogenase / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / zinc ion binding
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
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLamers MH / Schada von Borzyskowski L / Ren M
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Scholarship CouncilCSC202207720003 China
CitationJournal: To Be Published
Title: NAD-dependent dehydrogenase
Authors: Lamers MH / Schada von Borzyskowski L / Ren M
History
DepositionJun 5, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50545.png

Downloads & links

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Map

FileDownload / File: emd_50545.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRelion blush map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.037335843 - 0.07029121
Average (Standard dev.)0.00009998322 (±0.001873382)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.016 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_50545_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_50545_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PDEN_2367

EntireName: PDEN_2367
Components
  • Complex: PDEN_2367
    • Protein or peptide: alcohol dehydrogenase
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: PDEN_2367

SupramoleculeName: PDEN_2367 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Paracoccus denitrificans (bacteria)

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Macromolecule #1: alcohol dehydrogenase

MacromoleculeName: alcohol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: alcohol dehydrogenase
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Molecular weightTheoretical: 38.696234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH HHSSGHIEGR HNMAKTMKAA VVREFGKPLT IDEVPVPEPG PGMIQVRIQA SGVCHTDLHA AEGDWPVKPN PPFIPGHEG VGFVSAVGAG VKHVKEGDRV GVPWLYTACG HCRHCLGGWE TLCESQLNTG YSVNGGFADY VVADPNYVGH L PKNVDFLD ...String:
MGHHHHHHHH HHSSGHIEGR HNMAKTMKAA VVREFGKPLT IDEVPVPEPG PGMIQVRIQA SGVCHTDLHA AEGDWPVKPN PPFIPGHEG VGFVSAVGAG VKHVKEGDRV GVPWLYTACG HCRHCLGGWE TLCESQLNTG YSVNGGFADY VVADPNYVGH L PKNVDFLD IAPVLCAGVT VYKGLKVTDT KPGDWVVISG IGGLGHMAVQ YAKAMGMNVA AVDIDDEKLA LARKLGATVT VN AATEPDP AAAIRKQTDG GAQGVLVTAV GRKAFEQAIG MVARGGTVAL NGLPPGDFPL DIFGMVLNGI TVRGSIVGTR LDL QESLDF AGDGKVKATV HKAKLEDINN IFGQMHKGQI EGRMVLDMAG

UniProtKB: alcohol dehydrogenase

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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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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 206685
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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