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Yorodumi- EMDB-7969: 3D structure of the native alpha-crystallin from bovine eye lens. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7969 | |||||||||
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Title | 3D structure of the native alpha-crystallin from bovine eye lens. | |||||||||
Map data | Native alpha-crystallin from bovine eye lens. | |||||||||
Sample |
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Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 21.0 Å | |||||||||
Authors | Ryazantsev SN / Poliansky NB / Chebotareva NA / Muranov KO | |||||||||
Citation | Journal: Int J Biol Macromol / Year: 2018 Title: 3D structure of the native α-crystallin from bovine eye lens. Authors: Sergey N Ryazantsev / Nikolai B Poliansky / Natalia A Chebotareva / Konstantin O Muranov / Abstract: α-Crystallin is the major eye lens protein that has been shown to support lens transparency by preventing the aggregation of lens proteins. The 3D structure of α-crystallin is largely unknown. ...α-Crystallin is the major eye lens protein that has been shown to support lens transparency by preventing the aggregation of lens proteins. The 3D structure of α-crystallin is largely unknown. Electron microscopy, single-particle 3D reconstruction, size exclusion chromatography, dynamic light scattering, and analytical ultracentrifugation were used to study the structure of the native α-crystallin. Native α-crystallin has a wide distribution in size. The shape of mass distribution is temperature-dependent, but the oligomers with a sedimentation coefficient of ~22 S (750-830 kDa) strongly prevailed at all temperatures used. A 3D model of native α-crystallin with resolution of ~2 nm was created. The model is asymmetrical, has an elongated bean-like shape 13 × 19 nm with a dense core and filamentous "kernel". It does not contain a central cavity. The majority of α-crystallin particles regardless of experimental conditions are 13 × 19 nm, which corresponds to 22S sedimentation coefficient, hydrodynamic diameter 20 nm and mass of 750-830 kD. These particles are in dynamic equilibrium with particles of smaller and larger sizes. | |||||||||
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_7969.map.gz | 263.6 KB | EMDB map data format | |
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Header (meta data) | emd-7969-v30.xml emd-7969.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_7969.png | 101.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7969 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7969 | HTTPS FTP |
-Validation report
Summary document | emd_7969_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_7969_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_7969_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7969 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7969 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7969.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Native alpha-crystallin from bovine eye lens. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Native alpha-crystallin from bovine eye lens.
Entire | Name: Native alpha-crystallin from bovine eye lens. |
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Components |
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-Supramolecule #1: Native alpha-crystallin from bovine eye lens.
Supramolecule | Name: Native alpha-crystallin from bovine eye lens. / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bos taurus (cattle) / Organ: eye lens (cortex) |
Molecular weight | Experimental: 830 KDa |
-Macromolecule #1: Alpha-crystallin A chain CRYAA
Macromolecule | Name: Alpha-crystallin A chain CRYAA / type: protein_or_peptide / ID: 1 / Details: Alpha-crystallin A chain CRYAA / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) / Organ: eye lens (cortex) |
Sequence | String: MDIAIQHPWF KRTLGPFYP S RLFDQFFG EG LFEYDLL PFL SSTISP YYRQSLFRTV LDSG ISEVR SDRDK FVIF LDVKHF SPE DLTVKVQ ED FVEIHGKHNE RQDDHGYI S REFHRRYRL PSNVDQSALS CSLSADGML T FSGPKIPS GV DAGHSER AIP VSREEK PSSA PSS |
-Macromolecule #2: Alpha-crystallin B chain CRYAB
Macromolecule | Name: Alpha-crystallin B chain CRYAB / type: protein_or_peptide / ID: 2 / Details: Alpha-crystallin B chain CRYAB / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) / Organ: eye lens (cortex) |
Sequence | String: MDIAIHHPWI RRPFFPFHS P SRLFDQFF GE HLLESDL FPA STSLSP FYLRPPSFLR APSW IDTGL SEMRL EKDR FSVNLD VKH FSPEELK VK VLGDVIEVHG KHEERQDE H GFISREFHR KYRIPADVDP LAITSSLSS D GVLTVNGP RK QASGPER TIP ITREEK PAVT AAPKK |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.5 / Details: 20 mM Tris-HCl pH7.5, 100 mM NaCl, 1 mM EDTA |
Staining | Type: NEGATIVE / Material: urany acetate / Details: Valentine and double-carbon |
Grid | Model: Homemade / Material: COPPER / Mesh: 150 / Support film - Material: CARBON / Support film - topology: HOLEY |
Details | stored for 48 hr at 4oC prior usage |
-Electron microscopy
Microscope | JEOL 1200EX |
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Image recording | Film or detector model: GATAN MULTISCAN / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 1.9 mm |
Sample stage | Specimen holder model: JEOL |