3A68

Crystal structure of plant ferritin reveals a novel metal binding site that functions as a transit site for metal transfer in ferritin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.142 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of plant ferritin reveals a novel metal binding site that functions as a transit site for metal transfer in ferritin

Masuda, T., Goto, F., Yoshihara, T., Mikami, B.

(2010) J Biol Chem 285: 4049-4059

  • DOI: https://doi.org/10.1074/jbc.M109.059790
  • Primary Citation of Related Structures:  
    3A68, 3A9Q

  • PubMed Abstract: 

    Ferritins are important iron storage and detoxification proteins that are widely distributed in living kingdoms. Because plant ferritin possesses both a ferroxidase site and a ferrihydrite nucleation site, it is a suitable model for studying the mechanism of iron storage in ferritin. This article presents for the first time the crystal structure of a plant ferritin from soybean at 1.8-A resolution. The soybean ferritin 4 (SFER4) had a high structural similarity to vertebrate ferritin, except for the N-terminal extension region, the C-terminal short helix E, and the end of the BC-loop. Similar to the crystal structures of other ferritins, metal binding sites were observed in the iron entry channel, ferroxidase center, and nucleation site of SFER4. In addition to these conventional sites, a novel metal binding site was discovered intermediate between the iron entry channel and the ferroxidase site. This site was coordinated by the acidic side chain of Glu(173) and carbonyl oxygen of Thr(168), which correspond, respectively, to Glu(140) and Thr(135) of human H chain ferritin according to their sequences. A comparison of the ferroxidase activities of the native and the E173A mutant of SFER4 clearly showed a delay in the iron oxidation rate of the mutant. This indicated that the glutamate residue functions as a transit site of iron from the 3-fold entry channel to the ferroxidase site, which may be universal among ferritins.

    • Organizational Affiliation: 

    From the Laboratory of Food Quality Design and Development, Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011. Electronic address: masutaro@kais.kyoto-u.ac.jp.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin-4, chloroplastic
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
212Glycine maxMutation(s): 0 
EC: 1.16.3.1
UniProt
Find proteins for Q948P5 (Glycine max)
Explore Q948P5 
Go to UniProtKB:  Q948P5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ948P5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACY
Query on ACY
Download Ideal Coordinates CCD File 
DC [auth I]
EB [auth E]
FA [auth A]
FD [auth M]
GE [auth Q]
DC [auth I],
EB [auth E],
FA [auth A],
FD [auth M],
GE [auth Q],
IF [auth V],
KB [auth F],
KC [auth J],
ME [auth R],
OF [auth W],
QB [auth G],
SE [auth S],
TD [auth O],
VF [auth X],
WB [auth H],
YE [auth T],
ZC [auth L],
ZD [auth P]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth E]
AC [auth I]
AD [auth M]
AE [auth Q]
AA [auth A],
AB [auth E],
AC [auth I],
AD [auth M],
AE [auth Q],
AF [auth U],
BA [auth A],
BB [auth E],
BC [auth I],
BD [auth M],
BE [auth Q],
BF [auth U],
CA [auth A],
CB [auth E],
CC [auth I],
CD [auth M],
CE [auth Q],
CF [auth U],
DA [auth A],
DB [auth E],
DD [auth M],
DE [auth Q],
DF [auth V],
EA [auth A],
EC [auth J],
ED [auth M],
EE [auth Q],
EF [auth V],
FB [auth F],
FC [auth J],
FE [auth Q],
FF [auth V],
GA [auth B],
GB [auth F],
GC [auth J],
GD [auth N],
GF [auth V],
HA [auth B],
HB [auth F],
HC [auth J],
HD [auth N],
HE [auth R],
HF [auth V],
IA [auth B],
IB [auth F],
IC [auth J],
ID [auth N],
IE [auth R],
JA [auth B],
JB [auth F],
JC [auth J],
JD [auth N],
JE [auth R],
JF [auth W],
KA [auth B],
KD [auth N],
KE [auth R],
KF [auth W],
LA [auth C],
LB [auth G],
LC [auth K],
LD [auth N],
LE [auth R],
LF [auth W],
MA [auth C],
MB [auth G],
MC [auth K],
MD [auth O],
MF [auth W],
NA [auth C],
NB [auth G],
NC [auth K],
ND [auth O],
NE [auth S],
NF [auth W],
OA [auth C],
OB [auth G],
OC [auth K],
OD [auth O],
OE [auth S],
PA [auth C],
PB [auth G],
PC [auth K],
PD [auth O],
PE [auth S],
PF [auth X],
QA [auth C],
QC [auth K],
QD [auth O],
QE [auth S],
QF [auth X],
RA [auth C],
RB [auth H],
RC [auth K],
RD [auth O],
RE [auth S],
RF [auth X],
SA [auth D],
SB [auth H],
SC [auth L],
SD [auth O],
SF [auth X],
TA [auth D],
TB [auth H],
TC [auth L],
TE [auth T],
TF [auth X],
UA [auth D],
UB [auth H],
UC [auth L],
UD [auth P],
UE [auth T],
UF [auth X],
VA [auth D],
VB [auth H],
VC [auth L],
VD [auth P],
VE [auth T],
WA [auth D],
WC [auth L],
WD [auth P],
WE [auth T],
XA [auth E],
XB [auth I],
XC [auth L],
XD [auth P],
XE [auth T],
Y [auth A],
YA [auth E],
YB [auth I],
YC [auth L],
YD [auth P],
Z [auth A],
ZA [auth E],
ZB [auth I],
ZE [auth U]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.142 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.61α = 90
b = 220.886β = 90
c = 122.452γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description