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- PDB-9p35: Artemia ferritin in cell-free lysate with reverse His purification -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9p35
TitleArtemia ferritin in cell-free lysate with reverse His purification
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN
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 (arthropod)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.06 Å
AuthorsPowell, S.M. / Evans, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)EMSL S&T 60672 United States
CitationJournal: To Be Published
Title: Cryo-EM protein structure without purification
Authors: Powell, S.M. / Evans, J.E.
History
DepositionJun 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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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
U: Ferritin
V: Ferritin
W: Ferritin
X: Ferritin


Theoretical massNumber of molelcules
Total (without water)481,48224
Polymers481,48224
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Ferritin


Mass: 20061.744 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artemia franciscana (arthropod) / Gene: Fetn, QYM36_015043 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB PURExpress / References: UniProt: Q8WQM7, ferroxidase
Has protein modificationN

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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: Artemia ferritin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.481 MDa / Experimental value: NO
Source (natural)Organism: Artemia franciscana (arthropod)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: NEB PURExpress
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1300 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90000 / Symmetry type: POINT
RefinementHighest resolution: 2.06 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00334512
ELECTRON MICROSCOPYf_angle_d0.52246320
ELECTRON MICROSCOPYf_dihedral_angle_d3.9474560
ELECTRON MICROSCOPYf_chiral_restr0.0364800
ELECTRON MICROSCOPYf_plane_restr0.0046048

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