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- EMDB-75135: CryoEM structure of Aldehyde dehydrogenase from Francisella tular... -

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Basic information

Entry
Database: EMDB / ID: EMD-75135
TitleCryoEM structure of Aldehyde dehydrogenase from Francisella tularensis subsp. tularensis at 3.03A resolution
Map data
Sample
  • Complex: Aldehyde dehydrogenase
    • Protein or peptide: aldehyde dehydrogenase (NAD(+))
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity
Similarity search - Function
Aldehyde dehydrogenase family 7 member A1-like / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
aldehyde dehydrogenase (NAD(+))
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsAbendroth J / Davies DR / Yang M / Hoarnyi PS / Lorimer DD / Edwards TE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: To be published
Title: CryoEM structure of Aldehyde dehydrogenase from Francisella tularensis subsp. tularensis at 3.03A resolution
Authors: Abendroth J / Davies DR / Yang M / Hoarnyi PS / Lorimer DD / Edwards TE
History
DepositionJan 16, 2026-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75135.png

Downloads & links

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Map

FileDownload / File: emd_75135.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.2
Minimum - Maximum-0.9359717 - 1.6055782
Average (Standard dev.)0.00014030431 (±0.05252069)
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: #2

Fileemd_75135_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75135_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Aldehyde dehydrogenase

EntireName: Aldehyde dehydrogenase
Components
  • Complex: Aldehyde dehydrogenase
    • Protein or peptide: aldehyde dehydrogenase (NAD(+))

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Supramolecule #1: Aldehyde dehydrogenase

SupramoleculeName: Aldehyde dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Francisella tularensis subsp. tularensis (bacteria)

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Macromolecule #1: aldehyde dehydrogenase (NAD(+))

MacromoleculeName: aldehyde dehydrogenase (NAD(+)) / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: aldehyde dehydrogenase (NAD+)
Source (natural)Organism: Francisella tularensis subsp. tularensis (bacteria)
Molecular weightTheoretical: 55.559172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHMS ILKELDLGLQ AYITNDTNNV IETLNPATGE LLAKVRNQSV TTMQEAIAKA TEVAKQWRQV PAPKRGELVR LIDEELRRN KDHLGSLVSL EMGKSKQEGD GEVQEMIDMA DFAVGQSRML YGMMMNSERH NHRMYEQWHP LGVVGVISAF N FPVAVWSW ...String:
MAHHHHHHMS ILKELDLGLQ AYITNDTNNV IETLNPATGE LLAKVRNQSV TTMQEAIAKA TEVAKQWRQV PAPKRGELVR LIDEELRRN KDHLGSLVSL EMGKSKQEGD GEVQEMIDMA DFAVGQSRML YGMMMNSERH NHRMYEQWHP LGVVGVISAF N FPVAVWSW NAFIAVICGN TVVWKPSEKI PLCSIAVHNI CQKVIKEHNY PEIFYTVISK DVEVSKTLVN DERVNLVSFT GS TKVGQDV GQQVAKRFGK SILELGGNNA TIIDESANLK LAIPAAVFGA VGTAGQRCTS LRRLFIHESI YDLVKEKMVN AYK QVKVGD PLDQANLMGP LIDQAAVDNF TRTVEQAINQ GGKVLTGGKS IAKPGFFVEP TIIEANHNMP IVAEENFCPI LYIM PFKDI DEAIALNNSV IYGLSSSIFT DNLQNAEKFL SSLGSDCGIA NVNIGTSGAE IGGAFGGEKH TGGGREAGSD AWKAY MRRQ TSTINYGKDL PLAQGIKFNL GE

UniProtKB: aldehyde dehydrogenase (NAD(+))

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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 / Details: 10 mM HEPES pH 8.0, 150 mM NaCl, 1 mM NAD
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: new
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
Details: FrtuB.00020.a.B1.PS37973 was diluted from a 28.2 mg/ml to 10 mg/ml into dilution buffer (25 mM HEPES pH 8.0, 150 mM NaCl) and then further diluted to 1 mg/ml in diultion buffer supplemented ...Details: FrtuB.00020.a.B1.PS37973 was diluted from a 28.2 mg/ml to 10 mg/ml into dilution buffer (25 mM HEPES pH 8.0, 150 mM NaCl) and then further diluted to 1 mg/ml in diultion buffer supplemented with 1 mM NAD. 3 ul of mix were transferred on a Cu 300 QF R1.2/1.3 grid and vitrified in liquid ethane with a Vitrobot using the following parameter: 3 sec wait, 4 sec blot at blot force 7, 95% humidity, 5 C; data were collected on the PNCC Krios with a Falcon4i camera; CEM0001160JA..

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 15874 / Average exposure time: 1.0 sec. / 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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold2 model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 1078772
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

db-1


Chain - Residue range: 1-498 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-10fm:
CryoEM structure of Aldehyde dehydrogenase from Francisella tularensis subsp. tularensis at 3.03A resolution

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