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- PDB-9o8u: (1-methylalkyl)succinate synthase alpha-beta-gamma-delta complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9o8u | ||||||||||||||||||||||||||||||
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Title | (1-methylalkyl)succinate synthase alpha-beta-gamma-delta complex with bound fumarate | ||||||||||||||||||||||||||||||
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![]() | LYASE / glycyl radical enzyme / (1-methylalkyl)succinate synthase / X-succinate synthase / alkylsuccinate synthase / Hydrocarbon degradation / fumarate addition | ||||||||||||||||||||||||||||||
Function / homology | ![]() | ||||||||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||||||||||||||||||||
![]() | Andorfer, M.C. / Drennan, C.L. | ||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Anaerobic Alkane Activation by a Multi-Subunit Glycyl Radical Enzyme Authors: Andorfer, M.C. / Drennan, C.L. | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 322.6 KB | Display | ![]() |
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PDB format | ![]() | 256 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 58.8 KB | Display | |
Data in CIF | ![]() | 89.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 70238MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-1-methyl alkyl succinate synthase subunit ... , 3 types, 5 molecules AECFD
#1: Protein | Mass: 97053.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 6894.553 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | | Mass: 8033.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein , 1 types, 1 molecules B
#2: Protein | Mass: 13460.091 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 6 molecules 






#5: Chemical | ChemComp-FUM / | ||
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#6: Chemical | ChemComp-DTT / | ||
#7: Chemical | #8: Chemical | ChemComp-FE / | |
-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 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 | ||||||||||||||||||||
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Molecular weight | Value: 0.229 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 8 Details: 50 mM HEPES pH 8.0, 300 mM NaCl, 1 mM Fumarate, 1 mM DTT | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 1.42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 356678 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model |