[English] 日本語
Yorodumi
- PDB-9e8s: Structure of thioferritin (PfDPSL) with ferrihydrite growth at a ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9e8s
TitleStructure of thioferritin (PfDPSL) with ferrihydrite growth at a single three-fold pore.
ComponentsDNA protection during starvation protein
KeywordsMETAL BINDING PROTEIN / Ferritin / thioferritin / oxidative stress / iron homeostasis / iron mineral / ferric oxyhydroxide / mineral core / protein cage
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / nucleoid / ferroxidase activity / ferric iron binding / intracellular iron ion homeostasis / heme binding / DNA binding / cytosol
Similarity search - Function
: / DPS-like protein, ferritin-like diiron-binding domain / DNA-binding protein from starved cells-like / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / OXYGEN ATOM / OXYGEN MOLECULE / DNA protection during starvation protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsGauvin, C.C. / Waghwani, H.K. / Tokmina-Lukaszewska, M. / Bothner, B. / Douglas, T. / Lawrence, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DBI-1828765 United States
CitationJournal: J Am Chem Soc / Year: 2025
Title: The Mechanism of Mineral Nucleation and Growth in a Mini-Ferritin.
Authors: Colin C Gauvin / Monika Tokmina-Lukaszewska / Hitesh Kumar Waghwani / Sterling C McBee / Trevor Douglas / Brian Bothner / C Martin Lawrence /
Abstract: Iron is an enigmatic element. While necessary for life, as Fe(II) it also catalyzes formation of reactive oxygen species. To mitigate this, cellular life has evolved the ferritin protein superfamily, ...Iron is an enigmatic element. While necessary for life, as Fe(II) it also catalyzes formation of reactive oxygen species. To mitigate this, cellular life has evolved the ferritin protein superfamily, which includes the 24 subunit ferritins and bacterioferritins, and 12 subunit mini-ferritins (DPS). Each catalyze the oxidation of Fe(II) to ferric oxyhydroxide, which is then sequestered within the hollow protein shell. While there is a wealth of structural information on unmineralized ferritins, high resolution information on iron loaded ferritins is lacking, and the mechanism of iron mineralization is poorly understood. To address this, we followed iron loading in a mini-ferritin by cryo-EM. We determined a 1.86 Å structure in the unmineralized state, as well as a 1.91 Å structure of an early, iron loading state in which the mini-ferritin catalyzes nucleation of ferric oxyhydroxide at the acidic 3-fold pores. Mechanistically, a conserved crucible of precisely positioned glutamates and unsaturated main chain carbonyls are employed as a template to catalyze nucleation. A 2.4 Å structure at a later time point was also determined, revealing the role of a second constellation of main-chain carbonyls on the interior surface that subsequently supports crystalline mineral growth, that then proceeds into the center of the particle. Notably, the visualized mineral is consistent with one of two competing structural descriptions for ferrihydrite. This study provides the first pseudoatomic level observation of controlled mineral nucleation and growth in any member of the ferritin superfamily, and informs general mechanisms of nucleation and biomineralization.
History
DepositionNov 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
D: DNA protection during starvation protein
C: DNA protection during starvation protein
H: DNA protection during starvation protein
I: DNA protection during starvation protein
G: DNA protection during starvation protein
A: DNA protection during starvation protein
K: DNA protection during starvation protein
L: DNA protection during starvation protein
J: DNA protection during starvation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,38579
Polymers256,64712
Non-polymers2,73867
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
DNA protection during starvation protein


Mass: 21387.254 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: dps, PF1193 / Plasmid: pET-30a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8U1L3, Oxidoreductases; Oxidizing metal ions
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Thioferritin dodecamer with loaded ferroxidase centers and mineral at single 3-fold pore
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.256 MDa / Experimental value: YES
Source (natural)Organism: Pyrococcus furiosus (archaea)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) / Plasmid: pET-30a(+)
Buffer solutionpH: 6.5 / Details: 50 mM MES, 100 mM NaCl, pH 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-(N-morpholino)ethanesulfonic acidC6H13NO4S1
2100 mMSodium ChlorideNaCl1
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample formed a thin monodispersed layer.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 57000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9094

-
Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5particle selectionBlob picker was used to pick particles to train crYOLO model
2crYOLOparticle selection
3SerialEM4.1image acquisitionUsing SmartScope
5cryoSPARC4.5CTF correction
8UCSF ChimeraX1.8model fitting
10cryoSPARC4.5initial Euler assignment
11cryoSPARC4.5final Euler assignment
12cryoSPARC4.5classification
13cryoSPARC4.53D reconstruction
14PHENIX1.21.2_5419model refinement
Image processingDetails: Images were motion corrected using patch motion correction software in CryoSPARC.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3153592
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 395423 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 58.4 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Model was fit to map using ChimeraX fitmap, and then refined in PHENIX.
Atomic model buildingPDB-ID: 7STW

7stw


Accession code: 7STW / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more