1Z6O

Crystal Structure of Trichoplusia ni secreted ferritin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a secreted insect ferritin reveals a symmetrical arrangement of heavy and light chains.

Hamburger, A.E.West, A.P.Hamburger, Z.A.Hamburger, P.Bjorkman, P.J.

(2005) J Mol Biol 349: 558-569

  • DOI: https://doi.org/10.1016/j.jmb.2005.03.074
  • Primary Citation of Related Structures:  
    1Z6O

  • PubMed Abstract: 

    Ferritins are iron storage proteins made of 24 subunits forming a hollow spherical shell. Vertebrate ferritins contain varying ratios of heavy (H) and light (L) chains; however, known ferritin structures include only one type of chain and have octahedral symmetry. Here, we report the 1.9A structure of a secreted insect ferritin from Trichoplusia ni, which reveals equal numbers of H and L chains arranged with tetrahedral symmetry. The H/L-chain interface includes complementary features responsible for ordered assembly of the subunits. The H chain contains a ferroxidase active site resembling that of vertebrate H chains with an endogenous, bound iron atom. The L chain lacks the residues that form a putative iron core nucleation site in vertebrate L chains. Instead, a possible nucleation site is observed at the L chain 3-fold pore. The structure also reveals inter- and intrasubunit disulfide bonds, mostly in the extended N-terminal regions unique to insect ferritins. The symmetrical arrangement of H and L chains and the disulfide crosslinks reflect adaptations of insect ferritin to its role as a secreted protein.


  • Organizational Affiliation

    Division of Biology 114-96, California Institute of Technology, Pasadena, CA 91125, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin light chain
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
212Trichoplusia niMutation(s): 0 
UniProt
Find proteins for A0A7E5WUT2 (Trichoplusia ni)
Explore A0A7E5WUT2 
Go to UniProtKB:  A0A7E5WUT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7E5WUT2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin heavy chain
M, N, O, P, Q
M, N, O, P, Q, R, S, T, U, V, W, X
191Trichoplusia niMutation(s): 0 
UniProt
Find proteins for A0A7E5WTY7 (Trichoplusia ni)
Explore A0A7E5WTY7 
Go to UniProtKB:  A0A7E5WTY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7E5WTY7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
BA [auth B]
EA [auth C]
HA [auth F]
KA [auth M]
LA [auth N]
BA [auth B],
EA [auth C],
HA [auth F],
KA [auth M],
LA [auth N],
MA [auth O],
NA [auth P],
OA [auth Q],
PA [auth R],
QA [auth S],
RA [auth T],
SA [auth U],
TA [auth V],
UA [auth W],
VA [auth X],
Y [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth A]
CA [auth B]
DA [auth B]
FA [auth C]
GA [auth C]
AA [auth A],
CA [auth B],
DA [auth B],
FA [auth C],
GA [auth C],
IA [auth F],
JA [auth F],
Z [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.88α = 90
b = 145.697β = 94.93
c = 209.158γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description