8XWB | pdb_00008xwb

Crystal structure of dinitrosyl iron units binding with human heavy chain Ferritin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.195 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8XWB

This is version 1.0 of the entry. See complete history

Literature

Insight into the photodynamic mechanism and protein binding of a nitrosyl iron-sulfur [Fe 2 S 2 (NO) 4 ] 2- cluster.

Gong, W.Wu, T.Liu, Y.Jiao, S.Wang, W.Yan, W.Li, Y.Liu, Y.Zhang, Y.Wang, H.

(2024) Spectrochim Acta A Mol Biomol Spectrosc 320: 124603-124603

  • DOI: https://doi.org/10.1016/j.saa.2024.124603
  • Primary Citation Related Structures: 
    8XWB

  • PubMed Abstract: 

    Iron-sulfur cluster conversion and nitrosyl modification are involved in regulating their functions and play critical roles in signaling for biological systems. Hereby, the photo-induced dynamic process of (Me 4 N) 2 [Fe 2 S 2 (NO) 4 ] was monitored using time-resolved electron paramagnetic resonance (EPR) spectra, MS spectra and cellular imaging methods. Photo-irradiation and the solvent affect the reaction rates and products. Spectroscopic and kinetic studies have shown that the process involves at least three intermediates: spin-trapped NO free radical species with a g av at 2.040, and two other iron nitrosyl species, dinitrosyl iron units (DNICs) and mononitrosyl iron units (MNICs) with g av values at 2.031 and 2.024, respectively. Moreover, the [Fe 2 S 2 (NO) 4 ] 2- cluster could bind with ferritin and decompose gradually, and a binding state of dinitrosyl iron coordinated with Cys102 of the recombinant human heavy chain ferritin (rHuHF) was finally formed. This study provides insight into the photodynamic mechanism of nitrosyl iron - sulfur clusters to improve the understanding of physiological activity.


  • Organizational Affiliation
    • Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry and Key Laboratory of Energy Conversion and Storage Materials of Shanxi Provence, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China.

Macromolecule Content 

  • Total Structure Weight: 20.58 kDa 
  • Atom Count: 1,690 
  • Modeled Residue Count: 170 
  • Deposited Residue Count: 172 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferritin heavy chain172Homo sapiensMutation(s): 0 
Gene Names: FTH1FTHFTHL6OK/SW-cl.84PIG15
EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P02794 (Homo sapiens)
Explore P02794 
Go to UniProtKB:  P02794
PHAROS:  P02794
GTEx:  ENSG00000167996 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02794
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE
(Subject of Investigation/LOI)

Query on FE



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
(Subject of Investigation/LOI)

Query on CL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NO

Query on NO



Download:Ideal Coordinates CCD File
L [auth A],
M [auth A]
NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.195 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.68α = 90
b = 183.68β = 90
c = 183.68γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China62075118

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release