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- PDB-28yp: SpyTag-FtnA from E.Coli -

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Basic information

Entry
Database: PDB / ID: 28yp
TitleSpyTag-FtnA from E.Coli
ComponentsBacterial non-heme ferritin
KeywordsMETAL BINDING PROTEIN / Ferritin A
Function / homology
Function and homology information


bacterial non-heme ferritin / iron ion sequestering activity / ferroxidase activity / ferric iron binding / iron ion transport / cellular response to iron ion / ferrous iron binding / response to oxidative stress / intracellular iron ion homeostasis / DNA damage response ...bacterial non-heme ferritin / iron ion sequestering activity / ferroxidase activity / ferric iron binding / iron ion transport / cellular response to iron ion / ferrous iron binding / response to oxidative stress / intracellular iron ion homeostasis / DNA damage response / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Ferritin, prokaryotic-type / 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
Bacterial non-heme ferritin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsZimmermann, M. / Braun, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Biorxiv / Year: 2026
Title: Affinity-tag-based microfluidic protein isolation enables high-resolution Cryo-EM from minimal starting material
Authors: Zimmermann, M. / Braun, T.
History
DepositionMar 2, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterial non-heme ferritin
G: Bacterial non-heme ferritin
H: Bacterial non-heme ferritin
I: Bacterial non-heme ferritin
B: Bacterial non-heme ferritin
J: Bacterial non-heme ferritin
K: Bacterial non-heme ferritin
L: Bacterial non-heme ferritin
C: Bacterial non-heme ferritin
M: Bacterial non-heme ferritin
N: Bacterial non-heme ferritin
O: Bacterial non-heme ferritin
D: Bacterial non-heme ferritin
P: Bacterial non-heme ferritin
Q: Bacterial non-heme ferritin
R: Bacterial non-heme ferritin
E: Bacterial non-heme ferritin
S: Bacterial non-heme ferritin
T: Bacterial non-heme ferritin
U: Bacterial non-heme ferritin
F: Bacterial non-heme ferritin
V: Bacterial non-heme ferritin
W: Bacterial non-heme ferritin
X: Bacterial non-heme ferritin


Theoretical massNumber of molelcules
Total (without water)539,50124
Polymers539,50124
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Bacterial non-heme ferritin / Ferritin-1


Mass: 22479.229 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Details: homo 24-mer / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftnA, ftn, gen-165, rsgA, b1905, JW1893 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A998, bacterial non-heme ferritin
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: SpyTag-FtnA from E.Coli / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: Tris 50 mM , NaCl 50 mM, 1 mM EDTA, pH 7.5.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Details: cryoWriter

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4500
EM imaging opticsEnergyfilter name: TFS Selectris X

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
2EPUimage acquisition
4cryoSPARC4.7.1CTF correction
7UCSF ChimeraX1.11.1model fitting
9cryoSPARC4.7.1initial Euler assignment
10cryoSPARC4.7.1final Euler assignment
11cryoSPARC4.7.1classification
12cryoSPARC4.7.13D reconstruction
13PHENIX2model refinement
14Coot1.1.15model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 628929
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152336 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 1EUM

1eum


Accession code: 1EUM / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 17.46 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002532760
ELECTRON MICROSCOPYf_angle_d0.450644232
ELECTRON MICROSCOPYf_chiral_restr0.03424704
ELECTRON MICROSCOPYf_plane_restr0.00315712
ELECTRON MICROSCOPYf_dihedral_angle_d3.59094160

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