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- EMDB-74225: CryoEM structure of aldehyde dehydrogenase from Burkholderia ceno... -

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Basic information

Entry
Database: EMDB / ID: EMD-74225
TitleCryoEM structure of aldehyde dehydrogenase from Burkholderia cenocepacia at 2.33A resolution
Map dataCryoSPARC map from non-uniform refinement with D2 symmetry, sharpened map
Sample
  • Complex: homotetramer of aldehyde dehydrogenase from Burkholderia cenocepacia
    • Protein or peptide: Aldehyde dehydrogenase
  • Ligand: water
Keywordsaldehyde dehydrogenase / pathogenic bacteria / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / OXIDOREDUCTASE
Function / homology: / succinate-semialdehyde dehydrogenase (NAD+) activity / gamma-aminobutyric acid catabolic process / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / Aldehyde dehydrogenase
Function and homology information
Biological speciesBurkholderia cenocepacia J2315 (bacteria) / Burkholderia cenocepacia (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsDavies DR / Abendroth J / Yang M / Edwards TE / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: CryoEM structure of aldehyde dehydrogenase from Burkholderia cenocepacia at 2.33A resolution
Authors: Davies DR / Abendroth J / Yang M / Edwards TE / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionDec 3, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74225.png

Downloads & links

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Map

FileDownload / File: emd_74225.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoSPARC map from non-uniform refinement with D2 symmetry, sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 288 pix.
= 234.432 Å		0.81 Å/pix.
x 288 pix.
= 234.432 Å		0.81 Å/pix.
x 288 pix.
= 234.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.814 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.366
Minimum - Maximum-1.8023583 - 2.3690333
Average (Standard dev.)-0.00016025164 (±0.08767279)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 234.432 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: CryoSPARC map from non-uniform refinement with D2 symmetry,...

Fileemd_74225_half_map_1.map
AnnotationCryoSPARC map from non-uniform refinement with D2 symmetry, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoSPARC map from non-uniform refinement with D2 symmetry,...

Fileemd_74225_half_map_2.map
AnnotationCryoSPARC map from non-uniform refinement with D2 symmetry, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : homotetramer of aldehyde dehydrogenase from Burkholderia cenocepacia

EntireName: homotetramer of aldehyde dehydrogenase from Burkholderia cenocepacia
Components
  • Complex: homotetramer of aldehyde dehydrogenase from Burkholderia cenocepacia
    • Protein or peptide: Aldehyde dehydrogenase
  • Ligand: water

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Supramolecule #1: homotetramer of aldehyde dehydrogenase from Burkholderia cenocepacia

SupramoleculeName: homotetramer of aldehyde dehydrogenase from Burkholderia cenocepacia
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: aldehyde dehydrogenase from Burkholderia cenocepacia
Source (natural)Organism: Burkholderia cenocepacia J2315 (bacteria)

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Macromolecule #1: Aldehyde dehydrogenase

MacromoleculeName: Aldehyde dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Burkholderia cenocepacia (bacteria)
Molecular weightTheoretical: 50.941074 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MANVTYTDTQ LLIDGEWVDA ASGKTIDVVN PATGKPIGKV AHAGIADLDR ALAAAQRGFE AWRKVPAHER AATMRKAAAL VRERADTIA QLMTQEQGKP LTEARVEVLS AADIIEWFAD EGRRVYGRIV PPRNLGAQQT VVKEPVGPVA AFTPWNFPVN Q VVRKLSAA ...String:
MANVTYTDTQ LLIDGEWVDA ASGKTIDVVN PATGKPIGKV AHAGIADLDR ALAAAQRGFE AWRKVPAHER AATMRKAAAL VRERADTIA QLMTQEQGKP LTEARVEVLS AADIIEWFAD EGRRVYGRIV PPRNLGAQQT VVKEPVGPVA AFTPWNFPVN Q VVRKLSAA LATGCSFLVK APEETPASPA ALLRAFVDAG VPAGVIGLVY GDPAEISSYL IPHPVIRKVT FTGSTPVGKQ LA ALAGQHM KRATMELGGH APVIVAEDAD VALAVKAAGG AKFRNAGQVC ISPTRFLVHN SIRDEFTRAL VKHAEGLKVG NGL EEGTTL GALANPRRLT AMASVVDNAR KVGASIETGG ERIGAEGNFF APTVIANVPL EADVFNNEPF GPVAAIRGFD KLEE AIAEA NRLPFGLAGY AFTRSFANVH LLTQRLEVGM LWINQPATPW PEMPFGGVKD SGYGSEGGPE ALEPYLVTKS VTVMA V

UniProtKB: Aldehyde dehydrogenase

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 647 / 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

Concentration1 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8051 / 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 / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.2 µm
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: 8273271
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1703143
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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