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- EMDB-11272: Folding of an iron binding peptide in response to sedimentation i... -

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Basic information

Entry
Database: EMDB / ID: EMD-11272
TitleFolding of an iron binding peptide in response to sedimentation is resolved using ferritin as a nano-reactor
Map dataFerritin-M6A, with no treatment
Sample
  • Complex: Iron-loaded L-Ferritin-M6A
    • Protein or peptide: Ferritin
  • Ligand: FE (III) ION
KeywordsBiomineralization / nano-reactor / radiation damage assisted single-particle analysis / METAL BINDING PROTEIN
Function / homology
Function and homology information


ferric iron binding / iron ion transport / intracellular iron ion homeostasis
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / 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 speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDavidov G / Abelya G
Funding support Israel, 2 items
OrganizationGrant numberCountry
Israel Ministry of Science and Technology3-14335 Israel
Israel Ministry of Science and Technology Israel
CitationJournal: J Am Chem Soc / Year: 2020
Title: Folding of an Intrinsically Disordered Iron-Binding Peptide in Response to Sedimentation Revealed by Cryo-EM.
Authors: Geula Davidov / Gili Abelya / Ran Zalk / Benjamin Izbicki / Sharon Shaibi / Lior Spektor / Dayana Shagidov / Esther G Meyron-Holtz / Raz Zarivach / Gabriel A Frank /
Abstract: Biomineralization is mediated by specialized proteins that guide and control mineral sedimentation. In many cases, the active regions of these biomineralization proteins are intrinsically disordered. ...Biomineralization is mediated by specialized proteins that guide and control mineral sedimentation. In many cases, the active regions of these biomineralization proteins are intrinsically disordered. High-resolution structures of these proteins while they interact with minerals are essential for understanding biomineralization processes and the function of intrinsically disordered proteins (IDPs). Here we used the cavity of ferritin as a nanoreactor where the interaction between M6A, an intrinsically disordered iron-binding domain, and an iron oxide particle was visualized at high resolution by cryo-EM. Taking advantage of the differences in the electron-dose sensitivity of the protein and the iron oxide particles, we developed a method to determine the irregular shape of the particles found in our density maps. We found that the folding of M6A correlates with the detection of mineral particles in its vicinity. M6A interacts with the iron oxide particles through its C-terminal side, resulting in the stabilization of a helix at its N-terminal side. The stabilization of the helix at a region that is not in direct contact with the iron oxide particle demonstrates the ability of IDPs to respond to signals from their surroundings by conformational changes. These findings provide the first glimpse toward the long-suspected mechanism for biomineralization protein control over mineral microstructure, where unstructured regions of these proteins become more ordered in response to their interaction with the nascent mineral particles.
History
DepositionJul 1, 2020-
Header (metadata) releaseJul 14, 2021-
Map releaseJul 14, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0134
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0134
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zlq
  • Surface level: 0.0134
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zlq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11272.png

Downloads & links

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Map

FileDownload / File: emd_11272.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFerritin-M6A, with no treatment
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0134 / Movie #1: 0.0134
Minimum - Maximum-0.030646913 - 0.08758697
Average (Standard dev.)0.00029145225 (±0.003155444)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0310.0880.000

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Supplemental data

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Sample components

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Entire : Iron-loaded L-Ferritin-M6A

EntireName: Iron-loaded L-Ferritin-M6A
Components
  • Complex: Iron-loaded L-Ferritin-M6A
    • Protein or peptide: Ferritin
  • Ligand: FE (III) ION

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Supramolecule #1: Iron-loaded L-Ferritin-M6A

SupramoleculeName: Iron-loaded L-Ferritin-M6A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Nano cage L_ferritin_M6A at 0.1 mg per mL concentration after sodium acetate treatment with 0.044 mM FeCl2, Iron loaded
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Ferritin

MacromoleculeName: Ferritin / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.362076 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MTSQIRQNYS TEVEAAVNRL VNLHLRASYT YLSLGFFFDR DDVALEGVGH FFRELAEEKR EGAERLLEF QNDRGGRALF QDVQKPSQDE WGKTQEAMEA ALAMEKNLNQ ALLDLHALGS ARADPHLCDF LESHYLDKEV K LIKKMGNH ...String:
MGSSHHHHHH SSGLVPRGSH MTSQIRQNYS TEVEAAVNRL VNLHLRASYT YLSLGFFFDR DDVALEGVGH FFRELAEEKR EGAERLLEF QNDRGGRALF QDVQKPSQDE WGKTQEAMEA ALAMEKNLNQ ALLDLHALGS ARADPHLCDF LESHYLDKEV K LIKKMGNH LTNLRRVAGP QPAQTGAPQG SLGEYLFERL TLKHDGDIES AQSDEEVE

UniProtKB: Ferritin

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 16 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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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

Concentration0.1 mg/mL
BufferpH: 5.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 201772
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)

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