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- EMDB-54955: Cryo-EM structure of Human Apoferritin at pH 9 -

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Basic information

Entry
Database: EMDB / ID: EMD-54955
TitleCryo-EM structure of Human Apoferritin at pH 9
Map data
Sample
  • Complex: 24-mer of Human Apoferritin at pH 9
    • Protein or peptide: Ferritin heavy chain, N-terminally processed
  • Ligand: FE (III) ION
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsApoferritin / Ferritin / Metal storage / Low pH / 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 / autolysosome / negative regulation of ferroptosis / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / negative regulation of ferroptosis / ferroxidase activity / 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 / cytoplasm / cytosol
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: 1.89 Å
AuthorsSkalidis I / Semchonok DA / Tueting C / Hamdi F / Kastritis PL
Funding supportEuropean Union, Germany, Portugal, 12 items
OrganizationGrant numberCountry
European Union (EU)101086665European Union
German Federal Ministry for Education and Research03Z22HN23 Germany
German Federal Ministry for Education and Research03Z22HI2 Germany
German Federal Ministry for Education and Research03COV04 Germany
European Regional Development FundZS/2016/04/78115European Union
European Regional Development FundZS/2024/05/187255European Union
German Research Foundation (DFG)391498659 Germany
German Research Foundation (DFG)514901783 Germany
Fundacao para a Ciencia e a TecnologiaUIDB/04612/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/04612/2020 Portugal
Fundacao para a Ciencia e a TecnologiaLA/P/0087/2020 Portugal
H2020 Marie Curie Actions of the European Commission101207412European Union
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Direct evidence of acid-driven protein desolvation.
Authors: Farzad Hamdi / Ioannis Skalidis / Inken Kaja Schwerin / Jaydeep Belapure / Dmitry A Semchonok / Fotis L Kyrilis / Christian Tüting / Johannes Müller / Georg Künze / Panagiotis L Kastritis /
Abstract: Water and its ability to modulate the protonation states of biomolecules govern the physical chemistry of life, dictating their metabolic functions. However, how amino acid protonation alters protein ...Water and its ability to modulate the protonation states of biomolecules govern the physical chemistry of life, dictating their metabolic functions. However, how amino acid protonation alters protein hydration and solubility is an open question since Kuntz and Kauzmann proposed p-driven protein desolvation in 1974. Here, in a series of high-resolution cryoelectron microscopy structures of a protein complex at different p values (from p 9.0 to 3.5), we examined thousands of observable hydration sites. Cryoelectron microscopy data, in agreement with constant-p molecular dynamics simulations, show that nearly half of protein-bound waters exchanged with the bulk solvent upon acidification, with ~100 waters lost per p unit per molecule. The loss of waters was most significant around the side chains of glutamate and aspartate residues while specific polar residues, mostly asparagine, anchored persistent waters. A positionally conserved hydration layer was observed across all p conditions, accounting for 40% of resolved waters. Those waters displayed denser packing than less persistent waters, forming a p-independent solvation shell. Acid-induced water exchange also displaced bound iron, providing a mechanistic link between solvation and metal release. Our findings demonstrate the core principles of acid-driven protein desolvation, resolving a 50-y-old biochemical hypothesis.
History
DepositionSep 1, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54955.png

Downloads & links

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Map

FileDownload / File: emd_54955.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.59 Å/pix.
x 320 pix.
= 189.44 Å		0.59 Å/pix.
x 320 pix.
= 189.44 Å		0.59 Å/pix.
x 320 pix.
= 189.44 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.592 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.0172422 - 5.8597326
Average (Standard dev.)0.005530914 (±0.34974444)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 189.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54955_msk_1.map
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Half map: #2

Fileemd_54955_half_map_1.map
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Half map: #1

Fileemd_54955_half_map_2.map
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Sample components

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Entire : 24-mer of Human Apoferritin at pH 9

EntireName: 24-mer of Human Apoferritin at pH 9
Components
  • Complex: 24-mer of Human Apoferritin at pH 9
    • Protein or peptide: Ferritin heavy chain, N-terminally processed
  • Ligand: FE (III) ION
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: 24-mer of Human Apoferritin at pH 9

SupramoleculeName: 24-mer of Human Apoferritin at pH 9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: Ferritin heavy chain, N-terminally processed

MacromoleculeName: Ferritin heavy chain, N-terminally processed / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.1766 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
STSQVRQNYH QDSEAAINRQ INLELYASYV YLSMSYYFDR DDVALKNFAK YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDCDD WESGLNAMEC ALHLEKNVNQ SLLELHKLAT DKNDPHLCDF IETHYLSEQV KAIKELGDHV TNLRKMGAPE S GLAEYLFD KHTLG

UniProtKB: Ferritin heavy chain

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 1608 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 9
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 1867 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 438640
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio model
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 1.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 343262
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 300 / Software - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: UniProt ID: P02794
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9sjv:
Cryo-EM structure of Human Apoferritin at pH 9

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