[English] 日本語
Yorodumi
- EMDB-7969: 3D structure of the native alpha-crystallin from bovine eye lens. -

+
Open data


ID or keywords:

Loading...

-
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 (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

-
Structure visualization

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

emd_7969.png

Downloads & links

-
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.
Voxel sizeX=Y=Z: 4.3 Å
Density
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

-
Supplemental data

-
Sample components

-
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

-
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 (cattle) / Organ: eye lens (cortex)
Molecular weightExperimental: 830 KDa

-
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 (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

-
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 (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

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more