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- PDB-9o8u: (1-methylalkyl)succinate synthase alpha-beta-gamma-delta complex ... -

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Basic information

Entry
Database: PDB / ID: 9o8u
Title(1-methylalkyl)succinate synthase alpha-beta-gamma-delta complex with bound fumarate
Components
  • (1-methyl alkyl succinate synthase subunit ...) x 3
  • MasB protein
KeywordsLYASE / glycyl radical enzyme / (1-methylalkyl)succinate synthase / X-succinate synthase / alkylsuccinate synthase / Hydrocarbon degradation / fumarate addition
Function / homology
Function and homology information


lyase activity / cytosol
Similarity search - Function
Benzylsuccinate synthase gamma subunit / Benzylsuccinate synthase gamma subunit superfamily / BssC/TutF protein / : / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical ...Benzylsuccinate synthase gamma subunit / Benzylsuccinate synthase gamma subunit superfamily / BssC/TutF protein / : / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile.
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / FUMARIC ACID / IRON/SULFUR CLUSTER / MasB protein / 1-methyl alkyl succinate synthase subunit MasC / 1-methyl alkyl succinate synthase subunit MasD / 1-methyl alkyl succinate synthase subunit Mas E
Similarity search - Component
Biological speciesAzoarcus sp. HxN1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsAndorfer, M.C. / Drennan, C.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129882 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145910 United States
CitationJournal: To Be Published
Title: Structural Basis for Anaerobic Alkane Activation by a Multi-Subunit Glycyl Radical Enzyme
Authors: Andorfer, M.C. / Drennan, C.L.
History
DepositionApr 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 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

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Assembly

Deposited unit
A: 1-methyl alkyl succinate synthase subunit MasD
B: MasB protein
C: 1-methyl alkyl succinate synthase subunit MasC
D: 1-methyl alkyl succinate synthase subunit Mas E
E: 1-methyl alkyl succinate synthase subunit MasD
F: 1-methyl alkyl succinate synthase subunit MasC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,77012
Polymers229,3896
Non-polymers1,3816
Water00
1


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

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Components

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1-methyl alkyl succinate synthase subunit ... , 3 types, 5 molecules AECFD

#1: Protein 1-methyl alkyl succinate synthase subunit MasD / (1-methylalkyl)succinate synthase alpha chain


Mass: 97053.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azoarcus sp. HxN1 (bacteria) / Gene: masD / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: A9J4K4
#3: Protein 1-methyl alkyl succinate synthase subunit MasC / (1-methylalkyl)succinate synthase gamma chain


Mass: 6894.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azoarcus sp. HxN1 (bacteria) / Gene: masC / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: A9J4K2
#4: Protein 1-methyl alkyl succinate synthase subunit Mas E / (1-methylalkyl)succinate synthase delta chain


Mass: 8033.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azoarcus sp. HxN1 (bacteria) / Gene: masE / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: A9J4K6

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Protein , 1 types, 1 molecules B

#2: Protein MasB protein / (1-methylalkyl)succinate synthase beta chain


Mass: 13460.091 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azoarcus sp. HxN1 (bacteria) / Gene: masB / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: A9J4K0

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Non-polymers , 4 types, 6 molecules

#5: Chemical ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION

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Details

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: Heterodimer complex of MASS alpha with beta, gamma, delta subunits
Type: COMPLEX
Details: one alpha subunits binds beta, gamma, delta subunits, and the other alpha subunit bind only gamma subunits.
Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.229 MDa / Experimental value: NO
Source (natural)Organism: Azoarcus sp. HxN1 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: NiCo21-DE3
Buffer solutionpH: 8
Details: 50 mM HEPES pH 8.0, 300 mM NaCl, 1 mM Fumarate, 1 mM DTT
Buffer component
IDConc.NameBuffer-ID
150 mMHEPES1
2300 mMSodium Chloride1
31 mMFumarate1
41 mMDTT1
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
7UCSF ChimeraXmodel fitting
12RELION43D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 356678 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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