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- EMDB-7969: 3D structure of the native alpha-crystallin from bovine eye lens. -

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Basic information

Entry
Database: EMDB / ID: EMD-7969
Title3D structure of the native alpha-crystallin from bovine eye lens.
Map dataNative alpha-crystallin from bovine eye lens.
Sample
  • Organelle or cellular component: Native alpha-crystallin from bovine eye lens.
    • Protein or peptide: Alpha-crystallin A chain CRYAA
    • Protein or peptide: Alpha-crystallin B chain CRYAB
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsRyazantsev SN / Poliansky NB / Chebotareva NA / Muranov KO
CitationJournal: 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
DepositionJun 6, 2018-
Header (metadata) releaseJun 20, 2018-
Map releaseJun 20, 2018-
UpdateJul 4, 2018-
Current statusJul 4, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7969.png

Downloads & links

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Map

FileDownload / File: emd_7969.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNative alpha-crystallin from bovine eye lens.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.3 Å/pix.
x 84 pix.
= 361.2 Å		4.3 Å/pix.
x 84 pix.
= 361.2 Å		4.3 Å/pix.
x 84 pix.
= 361.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1. / Movie #1: 1
Minimum - Maximum-1.6346421 - 2.8797734
Average (Standard dev.)0.019830417 (±0.22397162)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-42-42-42
Dimensions848484
Spacing848484
CellA=B=C: 361.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.34.34.3
M x/y/z848484
origin x/y/z0.0000.0000.000
length x/y/z361.200361.200361.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-42-42-42
NC/NR/NS848484
D min/max/mean-1.6352.8800.020

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Supplemental data

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Sample components

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Entire : Native alpha-crystallin from bovine eye lens.

EntireName: Native alpha-crystallin from bovine eye lens.
Components
  • Organelle or cellular component: Native alpha-crystallin from bovine eye lens.
    • Protein or peptide: Alpha-crystallin A chain CRYAA
    • Protein or peptide: Alpha-crystallin B chain CRYAB

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Supramolecule #1: Native alpha-crystallin from bovine eye lens.

SupramoleculeName: Native alpha-crystallin from bovine eye lens. / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: eye lens (cortex)
Molecular weightExperimental: 830 KDa

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Macromolecule #1: Alpha-crystallin A chain CRYAA

MacromoleculeName: Alpha-crystallin A chain CRYAA / type: protein_or_peptide / ID: 1 / Details: Alpha-crystallin A chain CRYAA / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: eye lens (cortex)
SequenceString:
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

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Macromolecule #2: Alpha-crystallin B chain CRYAB

MacromoleculeName: Alpha-crystallin B chain CRYAB / type: protein_or_peptide / ID: 2 / Details: Alpha-crystallin B chain CRYAB / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: eye lens (cortex)
SequenceString:
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

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-HCl pH7.5, 100 mM NaCl, 1 mM EDTA
StainingType: NEGATIVE / Material: urany acetate / Details: Valentine and double-carbon
GridModel: Homemade / Material: COPPER / Mesh: 150 / Support film - Material: CARBON / Support film - topology: HOLEY
Detailsstored for 48 hr at 4oC prior usage

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Electron microscopy

MicroscopeJEOL 1200EX
Image recordingFilm or detector model: GATAN MULTISCAN / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 1.9 mm
Sample stageSpecimen holder model: JEOL

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Image processing

Particle selectionNumber selected: 18000
CTF correctionSoftware - Name: EMAN2
Startup modelType of model: NONE / Details: featureless ellipsoid
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 10000
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: EMAN2
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: EMAN2

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