6A4U

The first crystal structure of crustacean ferritin that is a hybrid type of H and L ferritin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The first crystal structure of crustacean ferritin that is a hybrid type of H and L ferritin

Masuda, T.Zang, J.Zhao, G.Mikami, B.

(2018) Protein Sci 27: 1955-1960

  • DOI: 10.1002/pro.3495
  • Primary Citation of Related Structures:  
    6A4U

  • PubMed Abstract: 
  • Ferritin, a ubiquitous iron storage protein, has a crucial role in innate immunity in arthropods, which have no adaptive immune system. Arthropods are thought to have two types of ferritin molecules: the secreted type and the cytosolic type. Here, we present the first crystal structure of ferritin from crustacean, kuruma prawn (Marsupenaeus japonicus), at 1 ...

    Ferritin, a ubiquitous iron storage protein, has a crucial role in innate immunity in arthropods, which have no adaptive immune system. Arthropods are thought to have two types of ferritin molecules: the secreted type and the cytosolic type. Here, we present the first crystal structure of ferritin from crustacean, kuruma prawn (Marsupenaeus japonicus), at 1.16 Å resolution. This shrimp ferritin (MjFer) is the cytosolic type, and its structure shows well-conserved ferritin fold composed of a 4-helix bundle that assembles into a cage-like 24-mer. The structure of MjFer was more similar to those of human and vertebrate ferritins than to that of the secreted-type arthropod ferritin from an insect. MjFer possesses both a ferroxidase site and a nucleation site, which are the main characteristics of vertebrate H and L chain ferritins, respectively. The first crystal structure of crustacean ferritin, MjFer, has exceptionally high quality that provides the detailed structural information of metal moving pathway in ferritin.


    Organizational Affiliation

    Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FerritinA, B, C, D, E, F169Penaeus japonicusMutation(s): 1 
EC: 1.16.3.1
UniProt
Find proteins for T2B7E1 (Penaeus japonicus)
Explore T2B7E1 
Go to UniProtKB:  T2B7E1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , LB [auth E] , MB [auth E] , NA [auth C] , P [auth A] , Q [auth A] , R [auth A] , 
AA [auth B],  BA [auth B],  LB [auth E],  MB [auth E],  NA [auth C],  P [auth A],  Q [auth A],  R [auth A],  UB [auth F],  VA [auth D],  VB [auth F],  WA [auth D],  Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth E] , BB [auth E] , CB [auth E] , DA [auth C] , DB [auth E] , EA [auth C] , EB [auth E] , FA [auth C] , 
AB [auth E],  BB [auth E],  CB [auth E],  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],  HA [auth C],  HB [auth E],  I [auth A],  IA [auth C],  IB [auth E],  J [auth A],  JA [auth C],  JB [auth E],  K [auth A],  KA [auth C],  KB [auth E],  L [auth A],  LA [auth C],  M [auth A],  MA [auth C],  N [auth A],  NB [auth F],  O [auth A],  OB [auth F],  PB [auth F],  QA [auth D],  QB [auth F],  RA [auth D],  RB [auth F],  S [auth B],  SA [auth D],  SB [auth F],  T [auth B],  TA [auth D],  TB [auth F],  U [auth B],  UA [auth D],  V [auth B],  W [auth B],  X [auth B],  Y [auth B],  ZA [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
OA [auth C], PA [auth C], WB [auth F], XA [auth D], YA [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.872α = 90
b = 124.872β = 90
c = 175.683γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP 15K07574

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references