[English] 日本語
Yorodumi
- EMDB-73901: Human Ferritin Heavy Chain in the presence of Mg-ATP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73901
TitleHuman Ferritin Heavy Chain in the presence of Mg-ATP
Map dataHuman Ferritin Heavy Chain in the presence of Mg-ATP - Sharpened map
Sample
  • Complex: Human Heavy Chain Ferritin
    • Protein or peptide: Ferritin heavy chain
  • Ligand: water
Keywordsiron storage / METAL BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.49 Å
AuthorsNannenga BL / Rejendran A / Henley S / Terashi G / Srivastava A / Kihara D / Bou-Abdallah F
Funding support United States, 2 items
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, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_73901.png

Downloads & links

-
Map

FileDownload / File: emd_73901.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Ferritin Heavy Chain in the presence of Mg-ATP - Sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 374.528 Å		0.73 Å/pix.
x 512 pix.
= 374.528 Å		0.73 Å/pix.
x 512 pix.
= 374.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7315 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.186
Minimum - Maximum-0.86896855 - 1.5558438
Average (Standard dev.)0.00009853224 (±0.033828568)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 374.528 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_73901_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_73901_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_73901_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human Heavy Chain Ferritin

EntireName: Human Heavy Chain Ferritin
Components
  • Complex: Human Heavy Chain Ferritin
    • Protein or peptide: Ferritin heavy chain
  • Ligand: water

-
Supramolecule #1: Human Heavy Chain Ferritin

SupramoleculeName: Human Heavy Chain Ferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 480 KDa

-
Macromolecule #1: Ferritin heavy chain

MacromoleculeName: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.255656 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString:
MTTASTSQVR QNYHQDSEAA INRQINLELY ASYVYLSMSY YFDRDDVALK NFAKYFLHQS HEEREHAEKL MKLQNQRGGR IFLQDIKKP DCDDWESGLN AMECALHLEK NVNQSLLELH KLATDKNDPH LCDFIETHYL NEQVKAIKEL GDHVTNLRKM G APESGLAE YLFDKHTLGD SDNES

UniProtKB: Ferritin heavy chain

-
Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 2499 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 10.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 639998
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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