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- EMDB-72095: CryoEM structure of methylmalonic acid semialdehyde dehydrogenase... -

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Basic information

Entry
Database: EMDB / ID: EMD-72095
TitleCryoEM structure of methylmalonic acid semialdehyde dehydrogenase from Burkholderia cenocepacia at 2.38A resolution
Map data
Sample
  • Complex: Tetrameric sample of purified Methylmalonic acid semialdehyde dehydrogenase
    • Protein or peptide: methylmalonate-semialdehyde dehydrogenase (CoA acylating)
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: water
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


methylmalonate-semialdehyde dehydrogenase (CoA-acylating) / methylmalonate-semialdehyde dehydrogenase (acylating, NAD) activity / thymine catabolic process / L-valine catabolic process
Similarity search - Function
Methylmalonate-semialdehyde dehydrogenase / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
methylmalonate-semialdehyde dehydrogenase (CoA acylating)
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.38 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 methylmalonic acid semialdehyde dehydrogenase from Burkholderia cenocepacia at 2.38A resolution
Authors: Abendroth J / Davies DR / Yang M / Hoarnyi PS / Lorimer DD / Edwards TE
History
DepositionAug 12, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72095.png

Downloads & links

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Map

FileDownload / File: emd_72095.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 256 pix.
= 227.84 Å		0.89 Å/pix.
x 256 pix.
= 227.84 Å		0.89 Å/pix.
x 256 pix.
= 227.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.57
Minimum - Maximum-1.8028625 - 2.7889354
Average (Standard dev.)-0.00045976366 (±0.11178121)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 227.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72095_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_72095_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 : Tetrameric sample of purified Methylmalonic acid semialdehyde deh...

EntireName: Tetrameric sample of purified Methylmalonic acid semialdehyde dehydrogenase
Components
  • Complex: Tetrameric sample of purified Methylmalonic acid semialdehyde dehydrogenase
    • Protein or peptide: methylmalonate-semialdehyde dehydrogenase (CoA acylating)
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: water

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Supramolecule #1: Tetrameric sample of purified Methylmalonic acid semialdehyde deh...

SupramoleculeName: Tetrameric sample of purified Methylmalonic acid semialdehyde dehydrogenase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Burkholderia cenocepacia (bacteria)

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Macromolecule #1: methylmalonate-semialdehyde dehydrogenase (CoA acylating)

MacromoleculeName: methylmalonate-semialdehyde dehydrogenase (CoA acylating)
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: methylmalonate-semialdehyde dehydrogenase (CoA-acylating)
Source (natural)Organism: Burkholderia cenocepacia (bacteria)
Molecular weightTheoretical: 55.120836 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MAHHHHHHMT TVPAYTSDAD VGHYLDGAPV AGRSGRFQDV FNPALGRAVR RVALAGNDEV ERAVASARAA FPAWADTPPI RRARVLHRF LQLMNEHRDT LAAIITAEHG KVFSDAQGEV ARGIDIIEFA CGVPQLLKGD FTDQVSTGID NWTMRQPLGV V AGITPFNF ...String:
MAHHHHHHMT TVPAYTSDAD VGHYLDGAPV AGRSGRFQDV FNPALGRAVR RVALAGNDEV ERAVASARAA FPAWADTPPI RRARVLHRF LQLMNEHRDT LAAIITAEHG KVFSDAQGEV ARGIDIIEFA CGVPQLLKGD FTDQVSTGID NWTMRQPLGV V AGITPFNF PCMVPCWMFP VALATGNTFV LKPSERDPSA ALFIADLLTQ AGLPAGVFNV VQGDKGAVDA LLDHPDVQAV SF VGSTPIA AYVQQRAVQS GKRVQALGGA KNHLVVMPDA NIDQAVDALI GAAYGSAGER CMAISIAVLV GDVADKIVPA VAE RARKLV IGDGMSPEVE MGPIVTGEAL KRIEGYIEQG VNEGAQLVVD GRGLRVPGRE AGFFTGGTLF DHVKPDMRIY KEEI FGPVL GCVRVKDFGE AVDLINAHEF GNGVSCFTSD GGIAREFARR IQVGMVGINV PIPVPMAWHG FGGWKKSLFG DMHAY GEEG VRFYTRQKSV MQRWSSSIGK GAEFAMPTAK

UniProtKB: methylmalonate-semialdehyde dehydrogenase (CoA acylating)

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Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 346 / 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 / 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: BuceA.00020.a.B1.PS01775 was diluted from 58 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 dilution buffer supplemented with ...Details: BuceA.00020.a.B1.PS01775 was diluted from 58 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 dilution buffer supplemented with 1 mM NAD. 3 uL of mix was transferred onto a Cu 300 QF R1.2/1.3 grid and vitrified in liquid ethane with a Vitrobot using the following parameters: 3 sec wait, 4 sec blot at blot force 7, 95% humidity, 5 C. Data were collected on the University of Washington Glacios equipped with a K3 camera; CEM0001125JA..

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4642 / Average exposure time: 5.0 sec. / Average electron dose: 47.3 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold2 model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2412495
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX
RefinementSpace: REAL / Target criteria: ‘’
Output model

PDB-9q0d:
CryoEM structure of methylmalonic acid semialdehyde dehydrogenase from Burkholderia cenocepacia at 2.38A resolution

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