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- PDB-9hq6: Structural insights in the HuHf@gold-monocarbene adduct: aurophil... -

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Basic information

Entry
Database: PDB / ID: 9hq6
TitleStructural insights in the HuHf@gold-monocarbene adduct: aurophilicity revealed in a biological context
ComponentsFerritin heavy chain
KeywordsMETAL BINDING PROTEIN / Iron / Gold / Metal transport / Metal storage / Anticancer drugs / Drug nanocarrier
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
: / 1-butyl-3-methyl-1H-imidazol-3-ium / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.51 Å
AuthorsCosottini, L. / Giachetti, A. / Guerri, A. / Martinez-Castillo, A. / Geri, A. / Zineddu, S. / Abrescia, N.G.A. / Messori, L. / Turano, P. / Rosato, A.
Funding support Italy, Spain, 3items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
M: Ferritin heavy chain
N: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
Q: Ferritin heavy chain
R: Ferritin heavy chain
S: Ferritin heavy chain
T: Ferritin heavy chain
V: Ferritin heavy chain
W: Ferritin heavy chain
X: Ferritin heavy chain
Y: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)529,237144
Polymers506,98724
Non-polymers22,250120
Water60,9633384
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: 21124.459 Da / Num. of mol.: 24 / Mutation: NONE
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 (E. coli) / References: UniProt: P02794, ferroxidase
#2: Chemical...
ChemComp-BM0 / 1-butyl-3-methyl-1H-imidazol-3-ium / 1-butyl-3-methylimidazolium


Mass: 139.218 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C8H15N2
Details: In this structure, 1-butyl-3-methyl-imidazole-2-ylidene is deprotonated at C2 (molecular formula: C8H14N2).
Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 96 / Source method: obtained synthetically / Formula: Au
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: HuHf@Au(NHC)| / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.506 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameBuffer-ID
10.137 MNaCl1
20.0027 MKCl1
30.01 MNa2HPO41
40.0018 MKH2PO41
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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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: 1800 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 1.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2736719 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 1.51 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00235664
ELECTRON MICROSCOPYf_angle_d0.48748216
ELECTRON MICROSCOPYf_dihedral_angle_d4.724824
ELECTRON MICROSCOPYf_chiral_restr0.0345040
ELECTRON MICROSCOPYf_plane_restr0.0036384

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