[English] 日本語

- EMDB-70238: (1-methylalkyl)succinate synthase alpha-beta-gamma-delta complex ... -
+
Open data
-
Basic information
Entry | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | (1-methylalkyl)succinate synthase alpha-beta-gamma-delta complex with bound fumarate | ||||||||||||
![]() | |||||||||||||
![]() |
| ||||||||||||
![]() | glycyl radical enzyme / (1-methylalkyl)succinate synthase / X-succinate synthase / alkylsuccinate synthase / Hydrocarbon degradation / fumarate addition / LYASE | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||
![]() | Andorfer MC / Drennan CL | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Structural Basis for Anaerobic Alkane Activation by a Multi-Subunit Glycyl Radical Enzyme Authors: Andorfer MC / Drennan CL | ||||||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 5.1 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 25.1 KB 25.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 152.2 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() ![]() | 49.7 MB 49.8 MB 49.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 701 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 700.5 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9o8uMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.17 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: #1
File | emd_70238_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_70238_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_70238_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Heterodimer complex of MASS alpha with beta, gamma, delta subunits
Entire | Name: Heterodimer complex of MASS alpha with beta, gamma, delta subunits |
---|---|
Components |
|
-Supramolecule #1: Heterodimer complex of MASS alpha with beta, gamma, delta subunits
Supramolecule | Name: Heterodimer complex of MASS alpha with beta, gamma, delta subunits type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: one alpha subunits binds beta, gamma, delta subunits, and the other alpha subunit bind only gamma subunits. |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 229 KDa |
-Macromolecule #1: 1-methyl alkyl succinate synthase subunit MasD
Macromolecule | Name: 1-methyl alkyl succinate synthase subunit MasD / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 97.053289 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSSHHHHHH SQMTATSTLS KTDLKNCETV EELRENQQWW WLAERERSAR LDYLRKATWK KGALGGNYFD GIRLDLEYPT LFTEAWKKY PNDPSMLRRA KATAYVLDNI SIFITDSAQL VGYVGSAPHT IAWRVDGAST VNSEVYNEPG IHAEPEAESL K KVAEINSY ...String: MGSSHHHHHH SQMTATSTLS KTDLKNCETV EELRENQQWW WLAERERSAR LDYLRKATWK KGALGGNYFD GIRLDLEYPT LFTEAWKKY PNDPSMLRRA KATAYVLDNI SIFITDSAQL VGYVGSAPHT IAWRVDGAST VNSEVYNEPG IHAEPEAESL K KVAEINSY WNGQTAVDKV GRLIDPEDAV KFFSGAIGWG TPSSAFGYSG KNFEYFMKGD RAFSQIIAEI DEKIDEAEEA TI GTPSPHI LPLYDKLNNW HAMKLVLEAA IRFAGRYARL ARVMAAKETD EQRKKELLRV AETCERVPAN PPRNLQESLQ YEH FVQVLA RYEAHEGAWP SRPDYYHGPL YAKDVEVEKN ITESEAIDLV GEYMIRCSEY GSFSPRYMRE GLQGVTGTFV WTLG GVNQD GTDACNGMTI ALLKAARLVR VANPTFGFRW HPKVSNEVLR ECFECIRQGL GYPTLRNDPV LIQNTMHWYG HPLEE ARTW VHMACMSPNP TTKHGTSPFR MASATMNSAK TIEYVLHNGY DRVVNMQMGP KTGDAREIKD FEDLFERWTV QLKWLM NLL VRTVNLGRFK DPEFFGRPFL SAITERAVEH GIDAVSPEGE RGNAWVTAFT WIENVDSMAA IKKLVFDDKK YTMSQLI DA LEAEWDGYEQ MRLDFVKNGP KWGNDDDYVD DIMLRCLSVA AEHSRNIQCT SGNCWPILPE NVSGNIHYAN IVGALPNG R RRGDALYDGG VSPGPGLDKA GPTAVLKSVG KIDHVNQGRS FLLNQRLSPT QLAGDKGFQL WNSYVRTWAE LGIDHIQFN VISDKVLRAA QNDPEGYQEV IVRVAGYSAH FIDISRKTQD NIIQRTVQGL GENLYFQG UniProtKB: 1-methyl alkyl succinate synthase subunit MasD |
-Macromolecule #2: MasB protein
Macromolecule | Name: MasB protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.460091 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSRRDEWKKL QEEMTRDGGE IKSLETVPEQ ACGICLNFTD NAYGSDGRGS CNVLKAGSNI SLPDVIITRS GENGYITFFN SDAKYCPNF ERMKLIDTDG HECADPISRR VQRQLSSIKK S UniProtKB: MasB protein |
-Macromolecule #3: 1-methyl alkyl succinate synthase subunit MasC
Macromolecule | Name: 1-methyl alkyl succinate synthase subunit MasC / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 6.894553 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: STCKECRNYF PINEEASRGD CVRRISDERQ SYYTARPTTE AAKCEGCSDY LENTRTAKAH UniProtKB: 1-methyl alkyl succinate synthase subunit MasC |
-Macromolecule #4: 1-methyl alkyl succinate synthase subunit Mas E
Macromolecule | Name: 1-methyl alkyl succinate synthase subunit Mas E / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 8.033105 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKCTECGHEA EVMKFRYHYN PRIDASLSLR QCPECQAVVT VDELKREVLG RMHNGDDPWG KSAGIENLAE G UniProtKB: 1-methyl alkyl succinate synthase subunit Mas E |
-Macromolecule #5: FUMARIC ACID
Macromolecule | Name: FUMARIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: FUM |
---|---|
Molecular weight | Theoretical: 116.072 Da |
Chemical component information | ![]() ChemComp-FUM: |
-Macromolecule #6: 2,3-DIHYDROXY-1,4-DITHIOBUTANE
Macromolecule | Name: 2,3-DIHYDROXY-1,4-DITHIOBUTANE / type: ligand / ID: 6 / Number of copies: 1 / Formula: DTT |
---|---|
Molecular weight | Theoretical: 154.251 Da |
Chemical component information | ![]() ChemComp-DTT: |
-Macromolecule #7: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 3 / Formula: SF4 |
---|---|
Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ![]() ChemComp-FS1: |
-Macromolecule #8: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: FE |
---|---|
Molecular weight | Theoretical: 55.845 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.8 mg/mL | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
Details: 50 mM HEPES pH 8.0, 300 mM NaCl, 1 mM Fumarate, 1 mM DTT | ||||||||||
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. | ||||||||||
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | TFS KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.42 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
---|---|
Refinement | Protocol: AB INITIO MODEL |
Output model | ![]() PDB-9o8u: |