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Yorodumi- EMDB-45309: CryoEM structure of Cryptococcus neoformans H99 Acetyl-CoA Synthe... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45309 | |||||||||
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Title | CryoEM structure of Cryptococcus neoformans H99 Acetyl-CoA Synthetase in complex with adenosine-5'-ethylphosphate | |||||||||
Map data | ||||||||||
Sample |
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Keywords | trimer / LIGASE | |||||||||
Function / homology | Function and homology information acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / mitochondrion / ATP binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Cryptococcus neoformans var. grubii H99 (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.37 Å | |||||||||
Authors | Xu Z / Schnicker NJ / Jezeski AJ / Krysan DJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: CryoEM structure of Cryptococcus neoformans H99 Acetyl-CoA Synthetase in complex with adenosine-5'-ethylphosphate Authors: Xu Z / Schnicker NJ / Jezeski AJ / Krysan DJ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_45309.map.gz | 49.6 MB | EMDB map data format | |
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Header (meta data) | emd-45309-v30.xml emd-45309.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_45309_fsc.xml | 7.8 KB | Display | FSC data file |
Images | emd_45309.png | 136.2 KB | ||
Filedesc metadata | emd-45309.cif.gz | 5.8 KB | ||
Others | emd_45309_half_map_1.map.gz emd_45309_half_map_2.map.gz | 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45309 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45309 | HTTPS FTP |
-Validation report
Summary document | emd_45309_validation.pdf.gz | 834.1 KB | Display | EMDB validaton report |
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Full document | emd_45309_full_validation.pdf.gz | 833.7 KB | Display | |
Data in XML | emd_45309_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_45309_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45309 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45309 | HTTPS FTP |
-Related structure data
Related structure data | 9c8sMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_45309.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.985 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map A
File | emd_45309_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_45309_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryptococcus neoformans H99 Acetyl-CoA Synthetase
Entire | Name: Cryptococcus neoformans H99 Acetyl-CoA Synthetase |
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Components |
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-Supramolecule #1: Cryptococcus neoformans H99 Acetyl-CoA Synthetase
Supramolecule | Name: Cryptococcus neoformans H99 Acetyl-CoA Synthetase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Cryptococcus neoformans var. grubii H99 (fungus) |
Molecular weight | Theoretical: 238 KDa |
-Macromolecule #1: Acetyl-coenzyme A synthetase
Macromolecule | Name: Acetyl-coenzyme A synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: acetate-CoA ligase |
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Source (natural) | Organism: Cryptococcus neoformans var. grubii H99 (fungus) |
Molecular weight | Theoretical: 77.47575 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MHHHHHHHHE NLYFQGKTEV APGVHHVHPL PDSVPESEDL FAPPPRMQGK EGRPKPHIGP NYESYVKEWA KTVGPNSDEW WAAKARETL DWYDDFKTVR AGGFEHGDVQ WFPEGTLNAA YNCLDRHYYK NPKKTAIIYE ADEPSESREV SYEELMQETC R VANVLKSY ...String: MHHHHHHHHE NLYFQGKTEV APGVHHVHPL PDSVPESEDL FAPPPRMQGK EGRPKPHIGP NYESYVKEWA KTVGPNSDEW WAAKARETL DWYDDFKTVR AGGFEHGDVQ WFPEGTLNAA YNCLDRHYYK NPKKTAIIYE ADEPSESREV SYEELMQETC R VANVLKSY GVKKGDAVSI YLPMTWQAAA AFLACARIGA IHSAVFAGFS AESLRDRVND CECKVLITTD EGRRGGKTIA TK QIVDAAL QQCPLVENVL VLRRTGNKVP MTEGRDKWWD EECAKMPAYC PCERMASEDP LFILYTSGST GKPKGVVHST AGY LLGTAL TLKYVFDAHP DDRFACMADI GWITGHSYII YGPLANGITT AVFESTPVYP TPSRYWDFVD KWKATQLYTA PTAI RLLRR MGEDHVKNHD LSSLRVLGSV GEPINPEAWH WYNDFAGKNQ CAIVDTYWMT ETGSISIAPL PGAISTKPGS ATFPF FGMD VDIIDPQTGQ VLEGNDVEGV LVARRPWPSI ARTVYRDHKR YLETYMKPYP GYFFFGDGAA RDYDGYMWIK GRVDDV INV SGHRLSTAEV ESALILHKGV AETAVVGCAD DLTGQAVYAF VTMKPEFDLK ATKEADLSKE LAIQVRKVIG PFAAPKK IY LVSDLPKTRS GKIMRRVLRK IVAGEGDQLG DLSSIADPQI VEEVKQKVTG SA UniProtKB: Acetyl-coenzyme A synthetase |
-Macromolecule #2: 5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine
Macromolecule | Name: 5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine / type: ligand / ID: 2 / Number of copies: 3 / Formula: WTA |
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Molecular weight | Theoretical: 375.274 Da |
Chemical component information | ChemComp-WTA: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
Details: 10 mM Tris pH7.5, 150 mM NaCl, 4mM MgCl2 and 10mM DTT | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.25 µm |