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- EMDB-11214: Folding of an iron binding peptide in response to sedimentation i... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11214 | |||||||||
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Title | Folding of an iron binding peptide in response to sedimentation is resolved using ferritin as a nano-reactor | |||||||||
![]() | M6A and sediment structure inside iron filled ferritin | |||||||||
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![]() | Biomineralization / nano-reactor / radiation damage assisted single-particle analysis / METAL BINDING PROTEIN | |||||||||
Function / homology | ![]() ferric iron binding / iron ion transport / intracellular iron ion homeostasis Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
![]() | Davidov G / Abelya G | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 56.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.9 KB 10.9 KB | Display Display | ![]() |
Images | ![]() | 78.9 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zh5MC ![]() 6z3dC ![]() 6zlgC ![]() 6zlqC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | M6A and sediment structure inside iron filled ferritin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Iron-loaded L-Ferritin-M6A
Entire | Name: Iron-loaded L-Ferritin-M6A |
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Components |
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-Supramolecule #1: Iron-loaded L-Ferritin-M6A
Supramolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Ferritin
Macromolecule | Name: Ferritin / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.362076 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 2 / Number of copies: 16 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 5.8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 178465 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8) |