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- EMDB-24707: High resolution map of molecular chaperone Artemin with C term His Tag -

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Basic information

Entry
Database: EMDB / ID: EMD-24707
TitleHigh resolution map of molecular chaperone Artemin with C term His Tag
Map data
Sample
  • Organelle or cellular component: 24mer complex with antiparallel dimers
Biological speciesArtemia franciscana (crustacean)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsParvate AD / Powell SM / Brookreason JT / Novikova IV / Evans JE
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)74914 United States
CitationJournal: Front Mol Biosci / Year: 2022
Title: Cryo-EM structure of the diapause chaperone artemin.
Authors: Amar D Parvate / Samantha M Powell / Jory T Brookreson / Trevor H Moser / Irina V Novikova / Mowei Zhou / James E Evans /
Abstract: The protein artemin acts as both an RNA and protein chaperone and constitutes over 10% of all protein in cysts during diapause. However, its mechanistic details remain elusive since no high- ...The protein artemin acts as both an RNA and protein chaperone and constitutes over 10% of all protein in cysts during diapause. However, its mechanistic details remain elusive since no high-resolution structure of artemin exists. Here we report the full-length structure of artemin at 2.04 Å resolution. The cryo-EM map contains density for an intramolecular disulfide bond between Cys22-Cys61 and resolves the entire C-terminus extending into the core of the assembled protein cage but in a different configuration than previously hypothesized with molecular modeling. We also provide data supporting the role of C-terminal helix F towards stabilizing the dimer form that is believed to be important for its chaperoning activity. We were able to destabilize this effect by placing a tag at the C-terminus to fully pack the internal cavity and cause limited steric hindrance.
History
DepositionAug 18, 2021-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24707.png

Downloads & links

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Map

FileDownload / File: emd_24707.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.3395 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.8270867 - 5.2274346
Average (Standard dev.)-0.0013020549 (±0.19337605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 135.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 24mer complex with antiparallel dimers

EntireName: 24mer complex with antiparallel dimers
Components
  • Organelle or cellular component: 24mer complex with antiparallel dimers

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Supramolecule #1: 24mer complex with antiparallel dimers

SupramoleculeName: 24mer complex with antiparallel dimers / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 705 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5 / Details: 1X TBS standard buffer
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 299 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6578 / Average exposure time: 1.5 sec. / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 792493
Initial angle assignmentType: PROJECTION MATCHING
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 660454

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

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