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- EMDB-56976: SpyTag-FtnA from E.Coli -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-56976
TitleSpyTag-FtnA from E.Coli
Map data
Sample
  • Complex: SpyTag-FtnA from E.Coli
    • Protein or peptide: Bacterial non-heme ferritin
KeywordsFerritin A / METAL BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsZimmermann M / Braun T
Funding support Switzerland, 1 items
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, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56976.png

Downloads & links

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Map

FileDownload / File: emd_56976.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0358
Minimum - Maximum-0.22019154 - 0.40290475
Average (Standard dev.)0.00018710642 (±0.014749402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 262.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56976_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56976_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SpyTag-FtnA from E.Coli

EntireName: SpyTag-FtnA from E.Coli
Components
  • Complex: SpyTag-FtnA from E.Coli
    • Protein or peptide: Bacterial non-heme ferritin

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Supramolecule #1: SpyTag-FtnA from E.Coli

SupramoleculeName: SpyTag-FtnA from E.Coli / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Bacterial non-heme ferritin

MacromoleculeName: Bacterial non-heme ferritin / type: protein_or_peptide / ID: 1 / Details: homo 24-mer / Number of copies: 24 / Enantiomer: LEVO / EC number: bacterial non-heme ferritin
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 22.479229 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHGSR GVPHIVMVDA YKRYKGSLKP EMIEKLNEQM NLELYSSLLY QQMSAWCSYH TFEGAAAFLR RHAQEEMTHM QRLFDYLTD TGNLPRINTV ESPFAEYSSL DELFQETYKH EQLITQKINE LAHAAMTNQD YPTFNFLQWY VSEQHEEEKL F KSIIDKLS LAGKSGEGLY FIDKELSTLD TQN

UniProtKB: Bacterial non-heme 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 / Details: Tris 50 mM , NaCl 50 mM, 1 mM EDTA, pH 7.5.
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Details: cryoWriter.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
SoftwareName: EPU
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 4500 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 628929
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab inito model
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 152336
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1eum


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.11.1)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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