2JD7

Crystal Structure of the Fe-soaked Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus furiosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of the Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus

Tatur, J.Hagen, W.R.Matias, P.M.

(2007) J Biol Inorg Chem 12: 615

  • DOI: https://doi.org/10.1007/s00775-007-0212-3
  • Primary Citation of Related Structures:  
    2JD6, 2JD7, 2JD8

  • PubMed Abstract: 

    The crystal structure of the ferritin from the archaeon, hyperthermophile and anaerobe Pyrococcus furiosus (PfFtn) is presented. While many ferritin structures from bacteria to mammals have been reported, until now only one was available from archaea, the ferritin from Archaeoglobus fulgidus (AfFtn). The PfFtn 24-mer exhibits the 432 point-group symmetry that is characteristic of most ferritins, which suggests that the 23 symmetry found in the previously reported AfFtn is not a common feature of archaeal ferritins. Consequently, the four large pores that were found in AfFtn are not present in PfFtn. The structure has been solved by molecular replacement and refined at 2.75-Angstrom resolution to R = 0.195 and R(free) = 0.247. The ferroxidase center of the aerobically crystallized ferritin contains one iron at site A and shows sites B and C only upon iron or zinc soaking. Electron paramagnetic resonance studies suggest this iron depletion of the native ferroxidase center to be a result of a complexation of iron by the crystallization salt. The extreme thermostability of PfFtn is compared with that of eight structurally similar ferritins and is proposed to originate mostly from the observed high number of intrasubunit hydrogen bonds. A preservation of the monomer fold, rather than the 24-mer assembly, appears to be the most important factor that protects the ferritin from inactivation by heat.


  • Organizational Affiliation

    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands. J.Tatur@tnw.tudelft.nl


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FERRITIN HOMOLOG174Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U2T8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U2T8 
Go to UniProtKB:  Q8U2T8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U2T8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AC [auth B]
BC [auth B]
CF [auth W]
DD [auth I]
ED [auth I]
AC [auth B],
BC [auth B],
CF [auth W],
DD [auth I],
ED [auth I],
FC [auth C],
GC [auth C],
HC [auth C],
ID [auth J],
IE [auth R],
JF [auth Y],
KF [auth Y],
ME [auth S],
PB [auth 8],
QA [auth 1],
QE [auth T],
UA [auth 2],
UC [auth G],
VC [auth G],
WB [auth A],
XE [auth V],
YA [auth 3],
YD [auth O],
YE [auth V],
ZA [auth 3],
ZC [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE
Query on FE

Download Ideal Coordinates CCD File 
AB [auth 4]
AD [auth I]
AE [auth P]
AF [auth W]
BB [auth 4]
AB [auth 4],
AD [auth I],
AE [auth P],
AF [auth W],
BB [auth 4],
BD [auth I],
BE [auth P],
BF [auth W],
CB [auth 4],
CC [auth C],
CD [auth I],
CE [auth Q],
DB [auth 5],
DC [auth C],
DE [auth Q],
DF [auth X],
EB [auth 5],
EC [auth C],
EE [auth Q],
EF [auth X],
FB [auth 5],
FD [auth J],
FE [auth R],
FF [auth X],
GB [auth 6],
GD [auth J],
GE [auth R],
GF [auth Y],
HB [auth 6],
HD [auth J],
HE [auth R],
HF [auth Y],
IB [auth 6],
IC [auth D],
IF [auth Y],
JB [auth 7],
JC [auth D],
JD [auth K],
JE [auth S],
KA [auth 0],
KB [auth 7],
KC [auth D],
KD [auth K],
KE [auth S],
LA [auth 0],
LB [auth 7],
LC [auth E],
LD [auth K],
LE [auth S],
LF [auth Z],
MA [auth 0],
MB [auth 8],
MC [auth E],
MD [auth L],
MF [auth Z],
NA [auth 1],
NB [auth 8],
NC [auth E],
ND [auth L],
NE [auth T],
NF [auth Z],
OA [auth 1],
OB [auth 8],
OC [auth F],
OD [auth L],
OE [auth T],
PA [auth 1],
PC [auth F],
PD [auth M],
PE [auth T],
QB [auth 9],
QC [auth F],
QD [auth M],
RA [auth 2],
RB [auth 9],
RC [auth G],
RD [auth M],
RE [auth U],
SA [auth 2],
SB [auth 9],
SC [auth G],
SD [auth N],
SE [auth U],
TA [auth 2],
TB [auth A],
TC [auth G],
TD [auth N],
TE [auth U],
UB [auth A],
UD [auth N],
UE [auth V],
VA [auth 3],
VB [auth A],
VD [auth O],
VE [auth V],
WA [auth 3],
WC [auth H],
WD [auth O],
WE [auth V],
XA [auth 3],
XB [auth B],
XC [auth H],
XD [auth O],
YB [auth B],
YC [auth H],
ZB [auth B],
ZD [auth P],
ZE [auth W]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 254.301α = 90
b = 342.878β = 90
c = 266.221γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description