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- PDB-6zlg: Folding of an iron binding peptide in response to sedimentation i... -

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Entry
Database: PDB / ID: 6zlg
TitleFolding of an iron binding peptide in response to sedimentation is resolved using ferritin as a nano-reactor
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Biomineralization / nano-reactor / radiation damage assisted single-particle analysis
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsDavidov, G. / Abelya, G. / Zalk, R. / Izbicki, B. / Shaibi, S. / Spektor, L. / Meyron Holtz, E.G. / Zarivach, R. / Frank, G.A.
Funding support Israel, 2items
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
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
O: Ferritin
P: Ferritin
Q: Ferritin
R: Ferritin
S: Ferritin
T: Ferritin
U: Ferritin
V: Ferritin
W: Ferritin
X: Ferritin
Y: Ferritin
Z: Ferritin


Theoretical massNumber of molelcules
Total (without water)584,69024
Polymers584,69024
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area89990 Å2
ΔGint-322 kcal/mol
Surface area141200 Å2
MethodPISA

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Components

#1: Protein ...
Ferritin


Mass: 24362.076 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ftl1, Ftl1-ps1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9CPX4

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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: Iron-loaded L-Ferritin-M6A / Type: COMPLEX
Details: Nano cage L_ferritin_M6A at 0.1 mg per mL concentration after sodium acetate treatment with 0.044 mM FeCl2, Iron loaded
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 5.8
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 80 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_3689: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELION3.0.8particle selection
2SerialEM2image acquisitionUsed by a home made script
4GctfCTF correction
10RELION3.0.8initial Euler assignment
11RELION3.0.8final Euler assignment
13RELION3.0.83D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98969 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00333560
ELECTRON MICROSCOPYf_angle_d0.36945064
ELECTRON MICROSCOPYf_dihedral_angle_d17.2644456
ELECTRON MICROSCOPYf_chiral_restr0.0314840
ELECTRON MICROSCOPYf_plane_restr0.0025944

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