7VHR | pdb_00007vhr

Apostichopus japonicus ferritin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 
    0.265 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Crystallographic characterization of a marine invertebrate ferritin from the sea cucumber Apostichopus japonicus.

Wu, Y.Ming, T.Huo, C.Qiu, X.Su, C.Lu, C.Zhou, J.Li, Y.Su, X.

(2022) FEBS Open Bio 12: 664-674

  • DOI: https://doi.org/10.1002/2211-5463.13375
  • Primary Citation Related Structures: 
    7VHR

  • PubMed Abstract: 

    Ferritin is considered to be an ubiquitous and conserved iron-binding protein that plays a crucial role in iron storage, detoxification, and immune response. Although ferritin is of critical importance for almost all kingdoms of life, there is a lack of knowledge about its role in the marine invertebrate sea cucumber (Apostichopus japonicus). In this study, we characterized the first crystal structure of A. japonicus ferritin (AjFER) at 2.75 Å resolution. The structure of AjFER shows a 4-3-2 symmetry cage-like hollow shell composed of 24 subunits, mostly similar to the structural characteristics of other known ferritin species, including the conserved ferroxidase center and 3-fold channel. The 3-fold channel consisting of three 3-fold negative amino acid rings suggests a potential pathway in which metal ions can be first captured by Asp120 from the outside environment, attracted by His116 and Cys128 when entering the channel, and then transferred by Glu138 from the 3-fold channel to the ferroxidase site. Overall, the presented crystal structure of AjFER may provide insights into the potential mechanism of the metal transport pathway for related marine invertebrate ferritins.


  • Organizational Affiliation
    • State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, China.

Macromolecule Content 

  • Total Structure Weight: 482.62 kDa 
  • Atom Count: 33,609 
  • Modeled Residue Count: 4,049 
  • Deposited Residue Count: 4,152 
  • 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, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
173Apostichopus japonicusMutation(s): 0 
Gene Names: BSL78_19566
EC: 1.16.3.1
UniProt
Find proteins for Q2QJV4 (Stichopus japonicus)
Explore Q2QJV4 
Go to UniProtKB:  Q2QJV4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2QJV4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth P]
BA [auth B]
BB [auth Q]
CA [auth C]
AA [auth B],
AB [auth P],
BA [auth B],
BB [auth Q],
CA [auth C],
CB [auth Q],
DA [auth D],
DB [auth R],
EA [auth D],
EB [auth S],
FA [auth E],
FB [auth S],
GA [auth E],
GB [auth S],
HA [auth E],
HB [auth T],
IA [auth F],
IB [auth U],
JA [auth G],
JB [auth V],
KA [auth H],
KB [auth W],
LA [auth H],
LB [auth X],
MA [auth I],
NA [auth J],
OA [auth J],
PA [auth K],
QA [auth K],
RA [auth L],
SA [auth M],
TA [auth N],
UA [auth N],
VA [auth N],
WA [auth N],
XA [auth O],
Y [auth A],
YA [auth O],
Z [auth A],
ZA [auth P]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free:  0.265 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.82α = 90
b = 178.78β = 90.26
c = 126.71γ = 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: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-05-18
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description