9KQK | pdb_00009kqk

Crystal structure of HSA in complex with AmpHecy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 
    0.340 (Depositor), 0.344 (DCC) 
  • R-Value Work: 
    0.290 (Depositor), 0.297 (DCC) 
  • R-Value Observed: 
    0.293 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Fluorogen-Activating Human Serum Albumin for Mitochondrial Nanoscale Imaging.

Fang, B.Bai, H.Zhang, J.Shi, M.Ge, Y.Wang, L.Li, P.Ding, Y.Zhang, S.Zhang, C.Qu, Y.Zhang, D.Peng, B.Chen, X.Li, L.Huang, W.

(2025) Adv Mater 37: e2501849-e2501849

  • DOI: https://doi.org/10.1002/adma.202501849
  • Primary Citation of Related Structures:  
    9KQK

  • PubMed Abstract: 

    Fluorescence nanoscopy of living cells employs contrast agents to reveal intrinsic correlations between mitochondrial dynamics and functions at the molecular level. However, regular mitochondrial fluorophores usually present poor photostability, low brightness, non-specific inhibitory effects, high phototoxicity, and rapid photobleaching, which have hindered the use of these tools to capture the intricate dynamic features of mitochondria. Herein, we engineered a fluorogen-activating protein (FAP), AmpHecy@HSA, a non-covalent self-assembly of HSA and amphiphilic hemicyanine (AmpHecy) fluorophore, with exceptional cell permeability, long-lasting photostability, high brightness/fluorogenicity, and minimal phototoxicity. Crystallography and femtosecond transient absorption spectroscopy techniques were combined to elucidate the structural and mechanistic intricacies of fluorescence activation. These findings revealed that fluorophore photoactivation happens through the molecular conformation-induced intramolecular charge transfer, whose kinetics is mainly determined by the hydrophobic interaction between the fluorophore and nearby amino acids. This aligns with classical molecular dynamics simulations and excited-state conformation quantum mechanics. It was further demonstrated that AmpHecy@HSA can be used for super-resolved images of mitochondria within living cells without apparent phototoxicity. This work expands the fluorescent toolkit based on FAP engineering for studying live-cell mitochondrial morphology and function, advancing the fields of chemistry and biomedicine.


  • Organizational Affiliation
    • State Key Laboratory of Flexible Electronics (LoFE) & Institute of Flexible Electronics (IFE), Xiamen University, Xiamen, 361102, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Albumin
A, B
609Homo sapiensMutation(s): 0 
Gene Names: ALBGIG20GIG42PRO0903PRO1708PRO2044PRO2619PRO2675UNQ696/PRO1341
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens)
Explore P02768 
Go to UniProtKB:  P02768
PHAROS:  P02768
GTEx:  ENSG00000163631 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02768
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EGK (Subject of Investigation/LOI)
Query on A1EGK

Download Ideal Coordinates CCD File 
C [auth B]2-[[6-[5-[(~{E})-2-[1-[2-[2-(2-methoxyethoxy)ethoxy]ethyl]pyridin-1-ium-4-yl]ethenyl]thiophen-2-yl]naphthalen-2-yl]-methyl-amino]ethanol
C31 H37 N2 O4 S
FMEDALDJBDBOTD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free:  0.340 (Depositor), 0.344 (DCC) 
  • R-Value Work:  0.290 (Depositor), 0.297 (DCC) 
  • R-Value Observed: 0.293 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.163α = 74.45
b = 58.406β = 88.13
c = 95.479γ = 76.18
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China21807088

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Database references
  • Version 1.2: 2025-12-03
    Changes: Database references