6LP5 | pdb_00006lp5

Structure of Sinonovacula constricta ferritin

• PDB DOI: https://doi.org/10.2210/pdb6LP5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinonovacula constricta
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-01-08 Released: 2020-04-08 
• Deposition Author(s): Su, X.R., Ming, T.H., Su, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.203 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

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

• PubMed: 31983429 
• DOI: https://doi.org/10.1016/j.bbrc.2020.01.069
• Primary Citation 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.

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Organizational Affiliation: 
• Zhejiang Collaborative Innovation Center for High Value Utilization of Byproducts from Ethylene Project, Ningbo Polytechnic, Ningbo, Zhejiang, 315800, China.
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, 315211, China; School of Marine Science, Ningbo University, Ningbo, Zhejiang, 315823, China. Electronic address: [e-mail].
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.
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, 315211, China; School of Marine Science, Ningbo University, Ningbo, Zhejiang, 315823, China.
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, 315211, China; School of Marine Science, Ningbo University, Ningbo, Zhejiang, 315823, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: scanning transmission electron microscopy

Macromolecule Content 

• Total Structure Weight: 120.07 kDa 
• Atom Count: 9,849 
• Modeled Residue Count: 1,020 
• Deposited Residue Count: 1,026 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A, B, C, D, E, F	171	Sinonovacula constricta	Mutation(s): 0  EC: 1.16.3.1
UniProt
Find proteins for D2JIV0 (Sinonovacula constricta) Explore D2JIV0  Go to UniProtKB:  D2JIV0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEZ	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)	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)	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 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.51	α = 90
b = 154.51	β = 90
c = 129.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
BALBES	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-08 
Deposition Author(s): Su, X.R., Ming, T.H., Su, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	41676159

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description