8ZN8 | pdb_00008zn8

MjF-3C-CdS QDs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.207 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Construction of An Artificial Photosynthesis System with A Single CdS QDs-Ferritin Hybrid Molecule.

Duan, M.Wang, Y.Zang, J.Lv, C.Du, M.Zhao, G.Zhang, T.

(2025) Small Methods 9: e2400915-e2400915

  • DOI: https://doi.org/10.1002/smtd.202400915
  • Primary Citation Related Structures: 
    8ZN8

  • PubMed Abstract: 

    Establishing artificial photosynthesis systems in a simple but effective manner to mitigate the greenhouse effect and address the energy crisis remains challenging. The combination of photocatalysis technology with bioengineering is an emerging field with great potential to construct such artificial photosynthesis systems, but so far, it has barely been explored in this area. Herein, an artificial photocatalysis platform is constructed with high CO 2 conversion and H 2 O splitting capability by integration of CdS QDs into the intra-subunit interface of H-type ferritin (Marsupenaeus japonicus), a natural ferroxidase through protein interface redesign. The crystal structure of the synthesized CdS QDs with engineered ferritin molecules as bio-templates confirmed the design at an atomic level. Notably, upon absorbing desirable visible light (≈420 nm), such a single CdS-ferritin hybrid molecule is able to selectively catalyze the reduction of CO 2 into HCOOH (≈90%), meanwhile catalyzing the oxidation of H 2 O into O 2 in an aqueous environment. The O 2 production rate reached to 180 µmol g -1  h -1 , and the HCOOH output hit almost 800 µmol g -1  h -1 . This work advances the utilization of the four-helix bundle structure for crafting artificial photosynthesis systems, facilitating the seamless integration of bioengineering and photocatalysis technology.


  • Organizational Affiliation
    • College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.

Macromolecule Content 

  • Total Structure Weight: 120.21 kDa 
  • Atom Count: 8,739 
  • Modeled Residue Count: 1,014 
  • Deposited Residue Count: 1,014 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferritin
A, B, C, D, E
A, B, C, D, E, F
169Penaeus japonicusMutation(s): 0 
EC: 1.16.3.1
UniProt
Find proteins for T2B7E1 (Penaeus japonicus)
Explore T2B7E1 
Go to UniProtKB:  T2B7E1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2B7E1
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on CD



Download:Ideal Coordinates CCD File
DA [auth C]
DB [auth E]
EA [auth C]
EB [auth E]
FA [auth C]
DA [auth C],
DB [auth E],
EA [auth C],
EB [auth E],
FA [auth C],
FB [auth E],
G [auth A],
GA [auth C],
GB [auth E],
H [auth A],
I [auth A],
J [auth A],
PA [auth D],
PB [auth F],
QA [auth D],
QB [auth F],
RA [auth D],
RB [auth F],
SA [auth D],
SB [auth F],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4
(Subject of Investigation/LOI)

Query on SO4



Download:Ideal Coordinates CCD File
CA [auth B]
CB [auth D]
OA [auth C]
OB [auth E]
R [auth A]
CA [auth B],
CB [auth D],
OA [auth C],
OB [auth E],
R [auth A],
S [auth A],
ZB [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
H2S
(Subject of Investigation/LOI)

Query on H2S



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
HA [auth C]
HB [auth E]
IA [auth C]
AA [auth B],
BA [auth B],
HA [auth C],
HB [auth E],
IA [auth C],
IB [auth E],
JA [auth C],
JB [auth E],
K [auth A],
KA [auth C],
KB [auth E],
L [auth A],
LA [auth C],
LB [auth E],
M [auth A],
MA [auth C],
MB [auth E],
N [auth A],
O [auth A],
P [auth A],
TA [auth D],
TB [auth F],
UA [auth D],
UB [auth F],
VA [auth D],
VB [auth F],
WA [auth D],
WB [auth F],
X [auth B],
XA [auth D],
XB [auth F],
Y [auth B],
YA [auth D],
Z [auth B],
ZA [auth D]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
AB [auth D]
BB [auth D]
NA [auth C]
NB [auth E]
Q [auth A]
AB [auth D],
BB [auth D],
NA [auth C],
NB [auth E],
Q [auth A],
YB [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.207 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.748α = 90
b = 126.748β = 90
c = 177.949γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2026-06-10
    Changes: Database references