6LP5

Structure of Sinonovacula constricta ferritin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystallographic characterization of ferritin from Sinonovacula constricta.

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

(2020) Biochem Biophys Res Commun 524: 217-223

  • DOI: https://doi.org/10.1016/j.bbrc.2020.01.069
  • Primary Citation of Related Structures:  
    6LP5

  • PubMed Abstract: 

    Ferritins are ubiquitous iron-binding proteins that are mainly related to iron storage, detoxification and innate immunity. Here, we present the crystal structure of a marine invertebrate ferritin from Sinonovacula constricta at a resolution of 1.98 Å. The S. constricta ferritin (ScFer) possessed some structural similarities with vertebrate ferritins, and they shared a well-conserved architecture composed of five α-helical bundles that assembled into a cage-like structure with 24-subunits. The structure of ScFer also showed iron binding sites in the 3-fold channel, ferroxidase center, and putative nucleation sites. Further, electrostatic potential calculations suggested that the electrostatic gradient of the 3-fold channel could provide a guidance mechanism for iron entering the ferritin cavity.


  • Organizational Affiliation

    Zhejiang Collaborative Innovation Center for High Value Utilization of Byproducts from Ethylene Project, Ningbo Polytechnic, Ningbo, Zhejiang, 315800, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin
A, B, C, D, E
A, B, C, D, E, F
171Sinonovacula constrictaMutation(s): 0 
EC: 1.16.3.1
UniProt
Find proteins for D2JIV0 (Sinonovacula constricta)
Explore D2JIV0 
Go to UniProtKB:  D2JIV0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2JIV0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
AA [auth F]
L [auth B]
O [auth C]
R [auth D]
U [auth E]
AA [auth F],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
V [auth E],
Z [auth F]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth B]
K [auth B]
M [auth C]
H [auth A],
I [auth A],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth D],
S [auth E],
T [auth E],
X [auth F],
Y [auth F]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
G [auth A],
W [auth F]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.51α = 90
b = 154.51β = 90
c = 129.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
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: 2020-04-08
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description