+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8743 | |||||||||
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Title | Rabbit muscle aldolase using 200keV | |||||||||
Map data | Final sharpened map of rabbit muscle aldolase | |||||||||
Sample |
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Keywords | glycolytic enzyme / LYASE | |||||||||
Function / homology | Function and homology information negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / fructose 1,6-bisphosphate metabolic process / I band / glycolytic process / protein homotetramerization / positive regulation of cell migration / cytosol Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Herzik Jr MA / Wu M / Lander GC | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Methods / Year: 2017 Title: Achieving better-than-3-Å resolution by single-particle cryo-EM at 200 keV. Authors: Mark A Herzik / Mengyu Wu / Gabriel C Lander / Abstract: Nearly all single-particle cryo-EM structures resolved to better than 4-Å resolution have been determined using 300-keV transmission electron microscopes (TEMs). We demonstrate that it is possible ...Nearly all single-particle cryo-EM structures resolved to better than 4-Å resolution have been determined using 300-keV transmission electron microscopes (TEMs). We demonstrate that it is possible to obtain reconstructions of macromolecular complexes of different sizes to better than 3-Å resolution using a 200-keV TEM. These structures are of sufficient quality to unambiguously assign amino acid rotameric conformations and identify ordered water molecules. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8743.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-8743-v30.xml emd-8743.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8743_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_8743.png | 60.1 KB | ||
Filedesc metadata | emd-8743.cif.gz | 6.5 KB | ||
Others | emd_8743_additional.map.gz emd_8743_half_map_1.map.gz emd_8743_half_map_2.map.gz | 7.4 MB 148.7 MB 149 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8743 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8743 | HTTPS FTP |
-Related structure data
Related structure data | 5vy5MC 8741C 8742C 5vy3C 5vy4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10181 (Title: Rabbit muscle aldolase movies obtained using Talos Arctica operating at 200 kV equipped with a K2 Data size: 1.5 TB Data #1: Raw, unaligned movie stacks of rabbit muscle aldolase acquired on a Talos Arctica using a K2 direct electron detector [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8743.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Final sharpened map of rabbit muscle aldolase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.91 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map of rabbit muscle aldolase
File | emd_8743_additional.map | ||||||||||||
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Annotation | Unsharpened map of rabbit muscle aldolase | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Rabbit muscle aldolase, odd half map
File | emd_8743_half_map_1.map | ||||||||||||
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Annotation | Rabbit muscle aldolase, odd half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Rabbit muscle aldolase, even half map
File | emd_8743_half_map_2.map | ||||||||||||
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Annotation | Rabbit muscle aldolase, even half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rabbit Muscle Aldolase
Entire | Name: Rabbit Muscle Aldolase |
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Components |
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-Supramolecule #1: Rabbit Muscle Aldolase
Supramolecule | Name: Rabbit Muscle Aldolase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Rabbit Muscle Aldolase (reconstituted from lyophilized form) |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Fructose-bisphosphate aldolase A
Macromolecule | Name: Fructose-bisphosphate aldolase A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: fructose-bisphosphate aldolase |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / Tissue: Muscle |
Molecular weight | Theoretical: 39.263672 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: PHSHPALTPE QKKELSDIAH RIVAPGKGIL AADESTGSIA KRLQSIGTEN TEENRRFYRQ LLLTADDRVN PCIGGVILFH ETLYQKADD GRPFPQVIKS KGGVVGIKVD KGVVPLAGTN GETTTQGLDG LSERCAQYKK DGADFAKWRC VLKIGEHTPS A LAIMENAN ...String: PHSHPALTPE QKKELSDIAH RIVAPGKGIL AADESTGSIA KRLQSIGTEN TEENRRFYRQ LLLTADDRVN PCIGGVILFH ETLYQKADD GRPFPQVIKS KGGVVGIKVD KGVVPLAGTN GETTTQGLDG LSERCAQYKK DGADFAKWRC VLKIGEHTPS A LAIMENAN VLARYASICQ QNGIVPIVEP EILPDGDHDL KRCQYVTEKV LAAVYKALSD HHIYLEGTLL KPNMVTPGHA CT QKYSHEE IAMATVTALR RTVPPAVTGV TFLSGGQSEE EASINLNAIN KCPLLKPWAL TFSYGRALQA SALKAWGGKK ENL KAAQEE YVKRALANSL ACQGKYTPSG QAGAAASESL FISNHAY UniProtKB: Fructose-bisphosphate aldolase A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.6 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.009000000000000001 kPa / Details: 15 Watts | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER Details: 3 uL of sample/grid was manually blotted for 4 seconds prior to immediate plunge-freezing in liquid nitrogen-cooled ethane.. | |||||||||
Details | Specimen was prepared from lyophilized rabbit muscle aldolase (Sigma Aldrich) |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 45000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Frames/image: 1-44 / Number grids imaged: 1 / Number real images: 810 / Average exposure time: 11.0 sec. / Average electron dose: 68.0 e/Å2 Details: Images collected using stage position navigation to target exposure. |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Details | Starting model was generated by stripping PDB entry 6ALD of all ligands and alternate conformations, then refining into the EM density using imposed symmetry while adjusting weighting/scoring according to estimated map resolution. The top 10 generated models (ranked based on quality metrics) were real-space refined using Phenix software. |
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Refinement | Space: REAL / Protocol: OTHER / Overall B value: 35 / Target criteria: Maximum Likelihood |
Output model | PDB-5vy5: |