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- PDB-9z91: Human Ferritin Heavy Chain in the presence of Mg-ATP -

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Basic information

Entry
Database: PDB / ID: 9z91
TitleHuman Ferritin Heavy Chain in the presence of Mg-ATP
ComponentsFerritin heavy chain
KeywordsMETAL BINDING PROTEIN / iron storage
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / negative regulation of ferroptosis / ferroxidase activity / autolysosome / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / negative regulation of ferroptosis / ferroxidase activity / autolysosome / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / Iron uptake and transport / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm
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
Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.49 Å
AuthorsNannenga, B.L. / Rejendran, A. / Henley, S. / Terashi, G. / Srivastava, A. / Kihara, D. / Bou-Abdallah, F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1942084 United States
National Science Foundation (NSF, United States)2435395 United States
CitationJournal: Int J Biol Macromol / Year: 2026
Title: Ferritin iron uptake and oxidation are dynamically modulated by nucleotide phosphate architecture via electrostatic gating.
Authors: Anitha Rajendran / Sean Henley / Brent L Nannenga / Genki Terashi / Ayush Srivastava / Daisuke Kihara / Fadi Bou-Abdallah /
Abstract: Ferritin safeguards cells from iron-induced oxidative stress by oxidizing and storing Fe within its nanocage, yet how its macromolecular architecture enables responsiveness to the cellular chemical ...Ferritin safeguards cells from iron-induced oxidative stress by oxidizing and storing Fe within its nanocage, yet how its macromolecular architecture enables responsiveness to the cellular chemical environment remains unclear. Here, we show that ferritin's iron-oxidation activity is modulated by an electrostatic gating mechanism centered at its 3-fold channels and sensitive to solution charge conditions representative of intracellular metabolites. At physiologically relevant nucleotide concentrations, ferritin-catalyzed Fe oxidation is strongly attenuated in the presence of triphosphate nucleotides, while diphosphates and monophosphates exert progressively weaker effects, indicating that ferritin responds selectively to the charge density and geometry of the phosphate chain, rather than nucleotide identity. High-resolution cryo-electron microscopy identifies condition-dependent differences in non-protein density within and near the ferritin 3-fold channels, consistent with changes in the local solvent and/or ion environment, rather than discrete ligand binding. Fluorescence and calorimetric measurements reveal weak, reversible nucleotide association (K ∼ 1 mM), supporting a low-affinity, dynamic electrostatic interaction mode. The inhibitory trend persists under reduced oxygen conditions and across ferritin assemblies with varying H/L composition, supporting physiological relevance across cellular oxygen tensions and native ferritin heteropolymers. Ferritin activity is similarly modulated in bacterial, yeast, and human cell lysates under near-physiological conditions, demonstrating the robustness of this behavior in complex environments. Together, these findings establish ferritin as a biological macromolecule whose intrinsic channel electrostatics enable reversible modulation of iron uptake and oxidation in response to its chemical environment.
History
DepositionNov 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Ferritin heavy chain
2: Ferritin heavy chain
4: Ferritin heavy chain
6: Ferritin heavy chain
A: Ferritin heavy chain
B: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
K: Ferritin heavy chain
M: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
Q: Ferritin heavy chain
S: Ferritin heavy chain
U: Ferritin heavy chain
W: Ferritin heavy chain
X: Ferritin heavy chain
Y: Ferritin heavy chain
a: Ferritin heavy chain
e: Ferritin heavy chain
r: Ferritin heavy chain


Theoretical massNumber of molelcules
Total (without water)510,13624
Polymers510,13624
Non-polymers00
Water45,0192499
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Ferritin heavy chain / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


Mass: 21255.656 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli B (bacteria) / References: UniProt: P02794, ferroxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2499 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: Human Heavy Chain Ferritin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: .48 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli B (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 10000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
4CTFFINDCTF correction
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 639998 / Symmetry type: POINT

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