+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28640 | |||||||||
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Title | Cryo-EM structure of Aldolase embedded in crystalline ice | |||||||||
Map data | The EM map of Aldolase embedded in crystalline ice frozen at -183 celsius degree. The resolution of EM map is 3.1 angstrom. | |||||||||
Sample |
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Keywords | Aldolase / Crystalline ice / 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 / I band / fructose 1,6-bisphosphate metabolic process / 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: 3.1 Å | |||||||||
Authors | Shi H / Wu C / Zhang X | |||||||||
Funding support | China, 1 items
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Citation | Journal: Structure / Year: 2023 Title: Addressing compressive deformation of proteins embedded in crystalline ice. Authors: Huigang Shi / Chunling Wu / Xinzheng Zhang / Abstract: For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. ...For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. Whether and how crystalline ice affects single-particle cryo-EM is still unclear. Here, single-particle cryo-EM was used to analyze three-dimensional structures of various proteins and viruses embedded in crystalline ice formed at various cooling rates. Low cooling rates led to shrinkage deformation and density distortions on samples having loose structures. Higher cooling rates reduced deformations. Deformation-free proteins in crystalline ice were obtained by modifying the freezing conditions, and reconstructions from these samples revealed a marked improvement over vitreous ice. This procedure also increased the efficiency of cryo-EM structure determinations and was essential for high-resolution reconstructions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28640.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-28640-v30.xml emd-28640.xml | 21.1 KB 21.1 KB | Display Display | EMDB header |
Images | emd_28640.png | 34 KB | ||
Masks | emd_28640_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-28640.cif.gz | 5.3 KB | ||
Others | emd_28640_additional_1.map.gz emd_28640_additional_2.map.gz emd_28640_additional_3.map.gz emd_28640_half_map_1.map.gz emd_28640_half_map_2.map.gz | 59.9 MB 48.4 MB 48.3 MB 48.4 MB 48.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28640 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28640 | HTTPS FTP |
-Validation report
Summary document | emd_28640_validation.pdf.gz | 970.6 KB | Display | EMDB validaton report |
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Full document | emd_28640_full_validation.pdf.gz | 970.2 KB | Display | |
Data in XML | emd_28640_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_28640_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28640 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28640 | HTTPS FTP |
-Related structure data
Related structure data | 8ew2MC 8bqnC 8ew0C 8f49C 8f7yC 8hhsC 8hi2C 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_28640.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The EM map of Aldolase embedded in crystalline ice frozen at -183 celsius degree. The resolution of EM map is 3.1 angstrom. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28640_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: The EM map of Aldolase embedded in vitreous...
File | emd_28640_additional_1.map | ||||||||||||
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Annotation | The EM map of Aldolase embedded in vitreous ice frozen at -183 celsius degree using standard procedure. The resolution of EM map is 3.4 angstrom. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: The half map of Aldolase embedded in vitreous...
File | emd_28640_additional_2.map | ||||||||||||
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Annotation | The half map of Aldolase embedded in vitreous ice frozen at -183 celsius degree using standard procedure. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: The half map of Aldolase embedded in vitreous...
File | emd_28640_additional_3.map | ||||||||||||
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Annotation | The half map of Aldolase embedded in vitreous ice frozen at -183 celsius degree using standard procedure. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: The half map of Aldolase embedded in crystalline...
File | emd_28640_half_map_1.map | ||||||||||||
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Annotation | The half map of Aldolase embedded in crystalline ice frozen at -183 celsius degree. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: The half map of Aldolase embedded in crystalline...
File | emd_28640_half_map_2.map | ||||||||||||
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Annotation | The half map of Aldolase embedded in crystalline ice frozen at -183 celsius degree. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Aldolase from rabbit
Entire | Name: Aldolase from rabbit |
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Components |
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-Supramolecule #1: Aldolase from rabbit
Supramolecule | Name: Aldolase from rabbit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
-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) |
Molecular weight | Theoretical: 39.263672 KDa |
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
Buffer | pH: 7.5 / Details: 20 mM HEPES pH 7.5, 50-mM NaCl |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |