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- EMDB-24706: High resolution map of molecular chaperone Artemin -

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Basic information

Entry
Database: EMDB / ID: EMD-24706
TitleHigh resolution map of molecular chaperone Artemin
Map dataUnsharpened map
Sample
  • Complex: 24mer Artemin complex
    • Protein or peptide: Ferritin
KeywordsMolecular chaperone Artemin is a homolog of apoferritin / CHAPERONE
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Biological speciesArtemia franciscana (crustacean)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.04 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-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24706.png

Downloads & links

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Map

FileDownload / File: emd_24706.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.34 Å/pix.
x 500 pix.
= 169.9 Å		0.34 Å/pix.
x 500 pix.
= 169.9 Å		0.34 Å/pix.
x 500 pix.
= 169.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.3398 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028
Minimum - Maximum-0.030969964 - 0.10143463
Average (Standard dev.)0.0012899501 (±0.0102147935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 169.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 24mer Artemin complex

EntireName: 24mer Artemin complex
Components
  • Complex: 24mer Artemin complex
    • Protein or peptide: Ferritin

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Supramolecule #1: 24mer Artemin complex

SupramoleculeName: 24mer Artemin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 624 MDa

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Macromolecule #1: Ferritin

MacromoleculeName: Ferritin / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 26.144912 KDa
Recombinant expressionOrganism: Triticum aestivum (bread wheat)
SequenceString: MATEGARNIG QSAPEGKVQM DCPSRHNFDP ECEKAFVEHI HLELASSYHA WSMWAFYARD CKAAVGMTRL CEWASHVSAQ RARRMAAYV LTRGGHVDYK EIPAPKKQGW DNFEDAFSHC VANKKRILTS LQSLYQCCQS KDAHCSNFIQ TDMMDEVIAW N KFLSDCLS ...String:
MATEGARNIG QSAPEGKVQM DCPSRHNFDP ECEKAFVEHI HLELASSYHA WSMWAFYARD CKAAVGMTRL CEWASHVSAQ RARRMAAYV LTRGGHVDYK EIPAPKKQGW DNFEDAFSHC VANKKRILTS LQSLYQCCQS KDAHCSNFIQ TDMMDEVIAW N KFLSDCLS NLHCIGSQGM GPWVFDRWLA RIVMSKFKHP KIPSLSTSDL ESNIPNELFD AEGDMVRAIK KL

UniProtKB: Ferritin

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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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2595 / Average exposure time: 1.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 167408
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 167408
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7rvb:
High resolution map of molecular chaperone Artemin

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