[English] 日本語
Yorodumi
- PDB-6t1r: Pseudo-atomic model of a 16-mer assembly of reduced recombinant h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t1r
TitlePseudo-atomic model of a 16-mer assembly of reduced recombinant human alphaA-crystallin (non domain swapped configuration)
ComponentsAlpha-crystallin A chain
KeywordsCHAPERONE / sHsp / alphaA-crystallin / domain swapping
Function / homology
Function and homology information


negative regulation of intracellular transport / structural constituent of eye lens / response to stimulus / visual perception / unfolded protein binding / protein stabilization / negative regulation of apoptotic process / structural molecule activity / protein-containing complex / nucleoplasm ...negative regulation of intracellular transport / structural constituent of eye lens / response to stimulus / visual perception / unfolded protein binding / protein stabilization / negative regulation of apoptotic process / structural molecule activity / protein-containing complex / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-crystallin, subunit A / Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone
Similarity search - Domain/homology
Alpha-crystallin A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.8 Å
AuthorsPeters, C. / Kaiser, C.J.O. / Weinkauf, S. / Zacharias, M. / Buchner, J.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationCRC 1035 Germany
German Research FoundationEXC 114 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: The structure and oxidation of the eye lens chaperone αA-crystallin.
Authors: Christoph J O Kaiser / Carsten Peters / Philipp W N Schmid / Maria Stavropoulou / Juan Zou / Vinay Dahiya / Evgeny V Mymrikov / Beate Rockel / Sam Asami / Martin Haslbeck / Juri Rappsilber / ...Authors: Christoph J O Kaiser / Carsten Peters / Philipp W N Schmid / Maria Stavropoulou / Juan Zou / Vinay Dahiya / Evgeny V Mymrikov / Beate Rockel / Sam Asami / Martin Haslbeck / Juri Rappsilber / Bernd Reif / Martin Zacharias / Johannes Buchner / Sevil Weinkauf /
Abstract: The small heat shock protein αA-crystallin is a molecular chaperone important for the optical properties of the vertebrate eye lens. It forms heterogeneous oligomeric ensembles. We determined the ...The small heat shock protein αA-crystallin is a molecular chaperone important for the optical properties of the vertebrate eye lens. It forms heterogeneous oligomeric ensembles. We determined the structures of human αA-crystallin oligomers by combining cryo-electron microscopy, cross-linking/mass spectrometry, NMR spectroscopy and molecular modeling. The different oligomers can be interconverted by the addition or subtraction of tetramers, leading to mainly 12-, 16- and 20-meric assemblies in which interactions between N-terminal regions are important. Cross-dimer domain-swapping of the C-terminal region is a determinant of αA-crystallin heterogeneity. Human αA-crystallin contains two cysteines, which can form an intramolecular disulfide in vivo. Oxidation in vitro requires conformational changes and oligomer dissociation. The oxidized oligomers, which are larger than reduced αA-crystallin and destabilized against unfolding, are active chaperones and can transfer the disulfide to destabilized substrate proteins. The insight into the structure and function of αA-crystallin provides a basis for understanding its role in the eye lens.
History
DepositionOct 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4894
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-crystallin A chain
B: Alpha-crystallin A chain
C: Alpha-crystallin A chain
D: Alpha-crystallin A chain
E: Alpha-crystallin A chain
F: Alpha-crystallin A chain
G: Alpha-crystallin A chain
H: Alpha-crystallin A chain
I: Alpha-crystallin A chain
J: Alpha-crystallin A chain
K: Alpha-crystallin A chain
L: Alpha-crystallin A chain
M: Alpha-crystallin A chain
N: Alpha-crystallin A chain
O: Alpha-crystallin A chain
P: Alpha-crystallin A chain


Theoretical massNumber of molelcules
Total (without water)318,98116
Polymers318,98116
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, microscopy, single particle EM (EMD-4894)
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area31980 Å2
ΔGint-148 kcal/mol
Surface area124490 Å2
MethodPISA

-
Components

#1: Protein
Alpha-crystallin A chain / Heat shock protein beta-4 / HspB4


Mass: 19936.314 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Details: wild type residues 1-166 / Source: (gene. exp.) Homo sapiens (human) / Tissue: lens / Gene: CRYAA, CRYA1, HSPB4 / Organ: eye / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: P02489

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Reduced recombinant human alphaA-crystallin / Type: COMPLEX
Details: Recombinant wild type full-length human alphaA-crystallin purified in the presence of reductant.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.319 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Cellular location: cytoplasm / Organ: eye / Tissue: lens
Source (recombinant)Organism: Escherichia coli BL21 (bacteria) / Plasmid: pET28
Buffer solutionpH: 7.4
Details: Buffer was prepared without EDTA and DTT. EDTA stock (500mM) was titrated to pH 8 and added to 1 mM. DTT stock (1M) was added to 1mM.
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMsodium chlorideNaClSodium chloride1
22.7 mMpotassium chlorideKCl1
38.1 mMsodium phosphate dibasicNa2HPO41
41.76 mMpotassium phosphate monobasicKH2PO41
51 mMEthylenediaminetetraacetic acidC10H16N2O81
61 mM1,4-DithiothreitC4H10O2S21
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Specimen was thawed, diluted to the final concentration and equilibrated at 310K for 3h.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Chamber temperature: 293 K
Details: Diluted equilibrated specimen was added to glow-discharged (30s) grids. Sample was blotted 30s after sample application and immediately plunged.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 37000 X / Calibrated magnification: 37037 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.2 sec. / Electron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3
EM imaging opticsEnergyfilter slit width: 10 eV
Image scansMovie frames/image: 10 / Used frames/image: 1-10

-
Processing

EM software
IDNameVersionCategory
1EMAN22particle selection
2TOMimage acquisition
4BsoftCTF correction
7Amber16model fitting
12IMAGIC53D reconstruction
13Amber16model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 74068 / Details: particles were picked manually
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19783 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Details: Structure created by homology modelling using PDB 3N3E and the N-terminal region (1-60) modelled using I-Tasser. The model was refined by flexible fitting into the EM density map EMD-4894. ...Details: Structure created by homology modelling using PDB 3N3E and the N-terminal region (1-60) modelled using I-Tasser. The model was refined by flexible fitting into the EM density map EMD-4894. The N-terminus is modelled only as CA atoms.
Atomic model buildingPDB-ID: 3N3E

3n3e


Accession code: 3N3E / Source name: PDB / Type: experimental model

+
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://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