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- PDB-10fm: CryoEM structure of Aldehyde dehydrogenase from Francisella tular... -

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Basic information

Entry
Database: PDB / ID: 10fm
TitleCryoEM structure of Aldehyde dehydrogenase from Francisella tularensis subsp. tularensis at 3.03A resolution
Componentsaldehyde 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsAbendroth, J. / Davies, D.R. / Yang, M. / Hoarnyi, P.S. / Lorimer, D.D. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
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, D.R. / Yang, M. / Hoarnyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 16, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aldehyde dehydrogenase (NAD(+))
B: aldehyde dehydrogenase (NAD(+))
C: aldehyde dehydrogenase (NAD(+))
D: aldehyde dehydrogenase (NAD(+))


Theoretical massNumber of molelcules
Total (without water)222,2374
Polymers222,2374
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 55559.172 Da / Num. of mol.: 4 / Fragment: BuceA.00020.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Gene: FTT_0552 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NHB4, aldehyde dehydrogenase (NAD+)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Aldehyde dehydrogenase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Francisella tularensis subsp. tularensis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 10 mM HEPES pH 8.0, 150 mM NaCl, 1 mM NAD
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: new / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K
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 imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15874
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
2EPUimage acquisition
4cryoSPARCCTF correction
12cryoSPARC4.7.03D reconstruction
13PHENIXdev_5420model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1078772 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingAccession code: 1 / Chain residue range: 1-498 / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.03 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00115128
ELECTRON MICROSCOPYf_angle_d0.38720531
ELECTRON MICROSCOPYf_dihedral_angle_d3.0612088
ELECTRON MICROSCOPYf_chiral_restr0.042372
ELECTRON MICROSCOPYf_plane_restr0.0032675

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