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- PDB-9q0d: CryoEM structure of methylmalonic acid semialdehyde dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 9q0d
TitleCryoEM structure of methylmalonic acid semialdehyde dehydrogenase from Burkholderia cenocepacia at 2.38A resolution
Componentsmethylmalonate-semialdehyde dehydrogenase (CoA acylating)
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / methylmalonate-semialdehyde dehydrogenase (CoA acylating)
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 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 methylmalonic acid semialdehyde dehydrogenase from Burkholderia cenocepacia at 2.38A resolution
Authors: Abendroth, J. / Davies, D.R. / Yang, M. / Hoarnyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionAug 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data 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: methylmalonate-semialdehyde dehydrogenase (CoA acylating)
B: methylmalonate-semialdehyde dehydrogenase (CoA acylating)
C: methylmalonate-semialdehyde dehydrogenase (CoA acylating)
D: methylmalonate-semialdehyde dehydrogenase (CoA acylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,1378
Polymers220,4834
Non-polymers2,6544
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "D"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_4ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11VALVALPHEPHEDD4 - 50012 - 508
d_12NADNADNADNADDH601
d_21VALVALPHEPHEAA4 - 50012 - 508
d_22NADNADNADNADAE601
d_31VALVALPHEPHECC4 - 50012 - 508
d_32NADNADNADNADCG601
d_41VALVALPHEPHEBB4 - 50012 - 508
d_42NADNADNADNADBF601

NCS oper:
IDCodeMatrixVector
1given(-0.99999999833725, 5.2183033309634E-5, 2.4544390870521E-5), (-5.2183893217195E-5, -0.99999999802468, -3.5035453717925E-5), (2.454256256579E-5, -3.5036734481542E-5, 0.99999999908504)227.83490863314, 227.84571247065, -0.00081565487818125
2given(-0.99999998779013, -0.00014801090125318, 5.0124909095723E-5), (-0.00014800906487707, 0.9999999883755, 3.6637726837736E-5), (-5.0130331296015E-5, 3.6630307449472E-5, -0.99999999807259)227.8516780606, 0.015731877920857, 226.06471957024
3given(0.99999999739335, -6.8381895734325E-5, 2.3177917703162E-5), (-6.837966700217E-5, -0.99999999304021, -9.6144722817371E-5), (2.318449210026E-5, 9.6143137668461E-5, -0.99999999510949)0.0012923674163119, 227.85444319619, 226.04855694463

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Components

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


Mass: 55120.836 Da / Num. of mol.: 4 / Fragment: BuceA.00020.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Gene: msdA, BCAL1439 / Plasmid: BuceA.00020.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B4E705, methylmalonate-semialdehyde dehydrogenase (CoA-acylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: Tetrameric sample of purified Methylmalonic acid semialdehyde dehydrogenase
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Burkholderia cenocepacia (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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: 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 imaging

MicroscopyModel: TFS GLACIOS
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: 5 sec. / Electron dose: 47.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4642

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10PHENIX2.0_5761model refinement
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2412495 / Symmetry type: POINT
Atomic model buildingSpace: REAL / Target criteria: ‘’
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 28.54 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002715472
ELECTRON MICROSCOPYf_angle_d0.530821024
ELECTRON MICROSCOPYf_chiral_restr0.0462308
ELECTRON MICROSCOPYf_plane_restr0.00442780
ELECTRON MICROSCOPYf_dihedral_angle_d10.7765728
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DDELECTRON MICROSCOPYNCS constraints4.725858725812E-13
ens_1d_3DDELECTRON MICROSCOPYNCS constraints2.4530556385961E-12
ens_1d_4DDELECTRON MICROSCOPYNCS constraints3.3604638602296E-12

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