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- EMDB-9913: Cryo-EM structure of Holo-bacterioferritin-form-I from Streptomyc... -

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Basic information

Entry
Database: EMDB / ID: EMD-9913
TitleCryo-EM structure of Holo-bacterioferritin-form-I from Streptomyces coelicolor
Map dataStructure of bacterioferritin holoform-I from Streptomyces coelicolor
Sample
  • Organelle or cellular component: Bacterioferritin in complex with HEME with Fe3 mineral core
    • Protein or peptide: Bacterioferritin
  • Ligand: FE (II) ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
KeywordsFerritin / Nanocage / Bacterioferritin / METAL TRANSPORT
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / iron ion transport / iron ion binding / heme binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / 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 speciesStreptomyces coelicolor (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsJobichen C / Sivaraman J
CitationJournal: To Be Published
Title: Cryo-EM structure of Apo-bacterioferritin from Streptomyces coelicolor.
Authors: Jobichen C / Sivaraman J
History
DepositionMay 23, 2019-
Header (metadata) releaseFeb 3, 2021-
Map releaseFeb 3, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6k43
  • Surface level: 5.1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6k43
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9913.png

Downloads & links

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Map

FileDownload / File: emd_9913.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of bacterioferritin holoform-I from Streptomyces coelicolor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 240 pix.
= 266.4 Å		1.11 Å/pix.
x 240 pix.
= 266.4 Å		1.11 Å/pix.
x 240 pix.
= 266.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.1 / Movie #1: 5.1
Minimum - Maximum-10.043312 - 18.853387999999999
Average (Standard dev.)0.029690271 (±1.2418478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 266.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z266.400266.400266.400
α/β/γ90.00090.00090.000
start NX/NY/NZ937643
NX/NY/NZ114126230
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-10.04318.8530.030

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Supplemental data

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Sample components

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Entire : Bacterioferritin in complex with HEME with Fe3 mineral core

EntireName: Bacterioferritin in complex with HEME with Fe3 mineral core
Components
  • Organelle or cellular component: Bacterioferritin in complex with HEME with Fe3 mineral core
    • Protein or peptide: Bacterioferritin
  • Ligand: FE (II) ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: Bacterioferritin in complex with HEME with Fe3 mineral core

SupramoleculeName: Bacterioferritin in complex with HEME with Fe3 mineral core
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptomyces coelicolor (bacteria)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: Bacterioferritin

MacromoleculeName: Bacterioferritin / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Streptomyces coelicolor (bacteria)
Molecular weightTheoretical: 19.242629 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MQGDPEVIEF LNEQLTAELT AINQYFLHAK LQDHKGWTKL AKYTRAESFD EMRHAEVLTD RILLLDGLPN YQRLFHVRVG QSVTEMFQA DREVELEAID RLRRGIEVMR AKHDITSANV FEAILADEEH HIDYLETQLD LIEKLGESLY LSTVIEQTQP D PSGPGSL

UniProtKB: Bacterioferritin

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Macromolecule #2: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 3 / Number of copies: 12 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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

Concentration1.8 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE
DetailsThis sample was monodisperse with 24mer nanocage assemblies.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5xx9

Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 19485
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cisTEM
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cisTEM
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5xx9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6k43:
Cryo-EM structure of Holo-bacterioferritin-form-I from Streptomyces coelicolor

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