7EMK | pdb_00007emk

Dendrorhynchus zhejiangensis ferritin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.188 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7EMK

This is version 1.2 of the entry. See complete history

Literature

Structure determination of ferritin from Dendrorhynchus zhejiangensis

Huan, H.S.Jiang, Q.Q.Wu, Y.Qiu, X.T.Lu, C.Y.Su, C.Zhou, J.Li, Y.Ming, T.H.Su, X.R.

(2020) Biochem Biophys Res Commun 531: 195-202

  • DOI: https://doi.org/10.1016/j.bbrc.2020.07.069
  • Primary Citation Related Structures: 
    7EMK

  • PubMed Abstract: 

    Ferritin is an important hub of iron metabolism because it stores iron during times of iron overload and releases iron during iron deficiency. Here, we present the first crystal structure of ferritin from the marine invertebrate Dendrorhynchus zhejiangensis with a 2.3 Å resolution. D. zhejiangensis ferritin (DzFer) exhibits a common cage-shaped hollow sphere with 24 subunits containing the ferroxidase centers and 3-fold and 4-fold channels. The structure of DzFer shows highly conserved catalytic residues in the ferroxidase center. The metal wire formed by ferrous ions in the 3-fold channel reveals the path that iron ions use to enter and translocate into the ferroxidase site to be oxidized and finally arrive at the nucleation site. However, the electrostatic environment of the channels and pores exhibits significant and extensive variability, suggesting that ferritins execute diverse functions in different environments.


  • Organizational Affiliation
    • State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, 315211, China; College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315823, China.

Macromolecule Content 

  • Total Structure Weight: 21.21 kDa 
  • Atom Count: 1,482 
  • Modeled Residue Count: 168 
  • Deposited Residue Count: 169 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dendrorhynchus zhejiangensis ferritin169Dendrorhynchus sinensisMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
VA [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
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]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
PA [auth A],
QA [auth A],
RA [auth A],
SA [auth A],
TA [auth A],
UA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.188 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.79α = 90
b = 151.79β = 90
c = 151.79γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
BALBESphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China41676159

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Derived calculations
  • Version 1.2: 2024-05-29
    Changes: Data collection, Database references