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- EMDB-52339: Structural insights in the HuHf@gold-monocarbene adduct: aurophil... -

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Basic information

Entry
Database: EMDB / ID: EMD-52339
TitleStructural insights in the HuHf@gold-monocarbene adduct: aurophilicity revealed in a biological context
Map data
Sample
  • Complex: HuHf@Au(NHC)|
    • Protein or peptide: Ferritin heavy chain
  • Ligand: 1-butyl-3-methyl-1H-imidazol-3-ium
  • Ligand: GOLD ION
  • Ligand: water
KeywordsIron / Gold / Metal transport / Metal storage / Anticancer drugs / Drug nanocarrier / METAL BINDING PROTEIN
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / 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 / membrane / 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: 1.51 Å
AuthorsCosottini L / Giachetti A / Guerri A / Martinez-Castillo A / Geri A / Zineddu S / Abrescia NGA / Messori L / Turano P / Rosato A
Funding support Italy, Spain, 3 items
OrganizationGrant numberCountry
Ministero dell Universita e della RicercaECS00000017 Italy
Ministero dell Universita e della RicercaIR0000009 Italy
Spanish Ministry of Economy and CompetitivenessPID2021-126130OB-I00 Spain
CitationJournal: Angew Chem Int Ed Engl / Year: 2025
Title: Structural Insight Into a Human H Ferritin@Gold-Monocarbene Adduct: Aurophilicity Revealed in a Biological Context.
Authors: Lucrezia Cosottini / Andrea Giachetti / Annalisa Guerri / Ane Martinez-Castillo / Andrea Geri / Stefano Zineddu / Nicola G A Abrescia / Luigi Messori / Paola Turano / Antonio Rosato /
Abstract: Human H ferritin (HuHf) has excellent potential as a nanocarrier for the selective delivery of anticancer metal-based drugs to tumor cells. Here, we addressed the interaction of the gold monocarbene ...Human H ferritin (HuHf) has excellent potential as a nanocarrier for the selective delivery of anticancer metal-based drugs to tumor cells. Here, we addressed the interaction of the gold monocarbene compound Au(NHC)Cl with HuHf by electrospray ionization-mass spectrometry (ESI-MS) measurements, which provide the metalation state of the protein subunits and demonstrate the involvement of protein cysteines in gold binding. The adduct between Au(NHC)Cl and HuHf was studied by cryo-EM measurements, resulting in a high-resolution 3D density map at 1.51 Å. The cryo-EM structure shows a novel tetranuclear gold(I) cluster, located in a surface pocket of each subunit where it is bound to Cys90 and Cys102. The short inter-metal distances are diagnostic of the occurrence of aurophilic interactions. The present work demonstrates the usefulness of cryo-EM to investigate the interactions between metal-based drugs and their protein targets/carriers, also leveraging the strong signal of transition metal ions.
History
DepositionDec 16, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52339.png

Downloads & links

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Map

FileDownload / File: emd_52339.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.51 Å/pix.
x 512 pix.
= 260.096 Å		0.51 Å/pix.
x 512 pix.
= 260.096 Å		0.51 Å/pix.
x 512 pix.
= 260.096 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.508 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.062353734 - 0.23002332
Average (Standard dev.)0.00080448895 (±0.008034691)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 260.096 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_52339_additional_1.map
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Half map: #2

Fileemd_52339_half_map_1.map
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Half map: #1

Fileemd_52339_half_map_2.map
Projections & Slices
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Sample components

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Entire : HuHf@Au(NHC)

EntireName: HuHf@Au(NHC)|
Components
  • Complex: HuHf@Au(NHC)|
    • Protein or peptide: Ferritin heavy chain
  • Ligand: 1-butyl-3-methyl-1H-imidazol-3-ium
  • Ligand: GOLD ION
  • Ligand: water

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Supramolecule #1: HuHf@Au(NHC)

SupramoleculeName: HuHf@Au(NHC)| / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 506 KDa

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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: 21.124459 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TTASTSQVRQ NYHQDSEAAI NRQINLELYA SYVYLSMSYY FDRDDVALKN FAKYFLHQSH EEREHAEKLM KLQNQRGGRI FLQDIKKPD CDDWESGLNA MECALHLEKN VNQSLLELHK LATDKNDPHL CDFIETHYLN EQVKAIKELG DHVTNLRKMG A PESGLAEY LFDKHTLGDS DNES

UniProtKB: Ferritin heavy chain

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Macromolecule #2: 1-butyl-3-methyl-1H-imidazol-3-ium

MacromoleculeName: 1-butyl-3-methyl-1H-imidazol-3-ium / type: ligand / ID: 2
Details: In this structure, 1-butyl-3-methyl-imidazole-2-ylidene is deprotonated at C2 (molecular formula: C8H14N2).
Number of copies: 24 / Formula: BM0
Molecular weightTheoretical: 139.218 Da
Chemical component information

ChemComp-BM0:
1-butyl-3-methyl-1H-imidazol-3-ium

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Macromolecule #3: GOLD ION

MacromoleculeName: GOLD ION / type: ligand / ID: 3 / Number of copies: 96 / Formula: AU
Molecular weightTheoretical: 196.967 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 3384 / 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

Concentration3 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
0.137 MNaCl
0.0027 MKCl
0.01 MNa2HPO4
0.0018 MKH2PO4
GridMaterial: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

13364

Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2736719
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9hq6:
Structural insights in the HuHf@gold-monocarbene adduct: aurophilicity revealed in a biological context

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