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

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Basic information

Entry
Database: PDB / ID: 7rvb
TitleHigh resolution map of molecular chaperone Artemin
ComponentsFerritin
KeywordsCHAPERONE / Molecular chaperone Artemin is a homolog of apoferritin
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.04 Å
AuthorsParvate, A.D. / Powell, S.M. / Brookreason, J.T. / Novikova, I.V. / Evans, J.E.
Funding support United States, 1items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
O: Ferritin
P: Ferritin
Q: Ferritin
R: Ferritin
S: Ferritin
T: Ferritin
V: Ferritin
W: Ferritin
X: Ferritin
Y: Ferritin


Theoretical massNumber of molelcules
Total (without water)627,47824
Polymers627,47824
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Ferritin


Mass: 26144.912 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artemia franciscana (crustacean) / Gene: Artn / Production host: Triticum aestivum (bread wheat) / References: UniProt: Q8WQM8, ferroxidase
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 24mer Artemin complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 624 MDa / Experimental value: YES
Source (natural)Organism: Artemia franciscana (crustacean)
Source (recombinant)Organism: Triticum aestivum (bread wheat)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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 FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2595
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
7PHENIXmodel fitting
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 167408
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167408 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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