4V6B

Crystal structure of human ferritin Phe167SerfsX26 mutant.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.249 

wwPDB Validation   3D Report Full Report


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


Literature

Unraveling of the E-helices and disruption of 4-fold pores are associated with iron mishandling in a mutant ferritin causing neurodegeneration

Baraibar, M.A., Muhoberac, B.B., Garringer, H.J., Hurley, T.D., Vidal, R.

(2010) J Biol Chem 285: 1950-1956

  • DOI: https://doi.org/10.1074/jbc.M109.042986
  • Primary Citation of Related Structures:  
    4V6B

  • PubMed Abstract: 

    • Mutations in the coding sequence of the ferritin light chain (FTL) gene cause a neurodegenerative disease known as neuroferritinopathy or hereditary ferritinopathy, which is characterized by the presence of intracellular inclusion bodies containing the mutant FTL polypeptide and by abnormal accumulation of iron in the brain ...

    Mutations in the coding sequence of the ferritin light chain (FTL) gene cause a neurodegenerative disease known as neuroferritinopathy or hereditary ferritinopathy, which is characterized by the presence of intracellular inclusion bodies containing the mutant FTL polypeptide and by abnormal accumulation of iron in the brain. Here, we describe the x-ray crystallographic structure and report functional studies of ferritin homopolymers formed from the mutant FTL polypeptide p.Phe167SerfsX26, which has a C terminus that is altered in amino acid sequence and length. The structure was determined and refined to 2.85 A resolution and was very similar to the wild type between residues Ile-5 and Arg-154. However, instead of the E-helices normally present in wild type ferritin, the C-terminal sequences of all 24 mutant subunits showed substantial amounts of disorder, leading to multiple C-terminal polypeptide conformations and a large disruption of the normally tiny 4-fold axis pores. Functional studies underscored the importance of the mutant C-terminal sequence in iron-induced precipitation and revealed iron mishandling by soluble mutant FTL homopolymers in that only wild type incorporated iron when in direct competition in solution with mutant ferritin. Even without competition, the amount of iron incorporation over the first few minutes differed severalfold. Our data suggest that disruption at the 4-fold pores may lead to direct iron mishandling through attenuated iron incorporation by the soluble form of mutant ferritin and that the disordered C-terminal polypeptides may play a major role in iron-induced precipitation and formation of ferritin inclusion bodies in hereditary ferritinopathy.

    Related Citations: 
    • Iron-mediated aggregation and a localized structural change characterize ferritin from a mutant light chain polypeptide that causes neurodegeneration.
      Baraibar, M.A., Barbeito, A.G., Muhoberac, B.B., Vidal, R.
      (2008) J Biol Chem 283: 31679
    Organizational Affiliation: 

    Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferritin
A [auth AA],
AA [auth AN],
AB [auth BC],
AC [auth BP],
AD [auth CE],
AE [auth CR],
B [auth Aa],
BA [auth An],
BB [auth Bc],
BC [auth Bp],
BD [auth Ce],
BE [auth Cr],
C [auth AB],
CA [auth AO],
CB [auth BD],
CC [auth BQ],
CD [auth CF],
CE [auth CS],
D [auth Ab],
DA [auth Ao],
DB [auth Bd],
DC [auth Bq],
DD [auth Cf],
DE [auth Cs],
E [auth AC],
EA [auth AP],
EB [auth BE],
EC [auth BR],
ED [auth CG],
EE [auth CT],
F [auth Ac],
FA [auth Ap],
FB [auth Be],
FC [auth Br],
FD [auth Cg],
FE [auth Ct],
G [auth AD],
GA [auth AQ],
GB [auth BF],
GC [auth BS],
GD [auth CH],
GE [auth CU],
H [auth Ad],
HA [auth Aq],
HB [auth Bf],
HC [auth Bs],
HD [auth Ch],
HE [auth Cu],
I [auth AE],
IA [auth AR],
IB [auth BG],
IC [auth BT],
ID [auth CI],
IE [auth CV],
J [auth Ae],
JA [auth Ar],
JB [auth Bg],
JC [auth Bt],
JD [auth Ci],
JE [auth Cv],
K [auth AF],
KA [auth AS],
KB [auth BH],
KC [auth BU],
KD [auth CJ],
KE [auth CW],
L [auth Af],
LA [auth As],
LB [auth Bh],
LC [auth Bu],
LD [auth Cj],
LE [auth Cw],
M [auth AG],
MA [auth AT],
MB [auth BI],
MC [auth BV],
MD [auth CK],
ME [auth CX],
N [auth Ag],
NA [auth At],
NB [auth Bi],
NC [auth Bv],
ND [auth Ck],
NE [auth Cx],
O [auth AH],
OA [auth AU],
OB [auth BJ],
OC [auth BW],
OD [auth CL],
P [auth Ah],
PA [auth Au],
PB [auth Bj],
PC [auth Bw],
PD [auth Cl],
Q [auth AI],
QA [auth AV],
QB [auth BK],
QC [auth BX],
QD [auth CM],
R [auth Ai],
RA [auth Av],
RB [auth Bk],
RC [auth Bx],
RD [auth Cm],
S [auth AJ],
SA [auth AW],
SB [auth BL],
SC [auth CA],
SD [auth CN],
T [auth Aj],
TA [auth Aw],
TB [auth Bl],
TC [auth Ca],
TD [auth Cn],
U [auth AK],
UA [auth AX],
UB [auth BM],
UC [auth CB],
UD [auth CO],
V [auth Ak],
VA [auth Ax],
VB [auth Bm],
VC [auth Cb],
VD [auth Co],
W [auth AL],
WA [auth BA],
WB [auth BN],
WC [auth CC],
WD [auth CP],
X [auth Al],
XA [auth Ba],
XB [auth Bn],
XC [auth Cc],
XD [auth Cp],
Y [auth AM],
YA [auth BB],
YB [auth BO],
YC [auth CD],
YD [auth CQ],
Z [auth Am],
ZA [auth Bb],
ZB [auth Bo],
ZC [auth Cd],
ZD [auth Cq]
192Homo sapiensMutation(s): 0 
Gene Names: FTL
UniProt
Find proteins for Q6S4P3 (Homo sapiens)
Explore Q6S4P3 
Go to UniProtKB:  Q6S4P3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6S4P3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
AF [auth AL],
AG [auth CE],
BF [auth AM],
BG [auth Ce],
CF [auth An],
AF [auth AL],
AG [auth CE],
BF [auth AM],
BG [auth Ce],
CF [auth An],
CG [auth CF],
DF [auth AO],
DG [auth Cg],
EF [auth BA],
EG [auth CH],
FF [auth Ba],
FG [auth Ck],
GF [auth BB],
GG [auth Cl],
HF [auth Bb],
HG [auth Cn],
IF [auth BC],
IG [auth CO],
JF [auth Bc],
JG [auth Cp],
KF [auth BD],
LF [auth Bd],
MF [auth Be],
NF [auth Bf],
OE [auth AA],
OF [auth BG],
PE [auth Aa],
PF [auth Bg],
QE [auth AB],
QF [auth BH],
RE [auth AC],
RF [auth BN],
SE [auth Ac],
SF [auth BR],
TE [auth Ad],
TF [auth Bu],
UE [auth Ae],
UF [auth CA],
VE [auth AF],
VF [auth Ca],
WE [auth Ag],
WF [auth CB],
XE [auth AH],
XF [auth Cb],
YE [auth Ah],
YF [auth CC],
ZE [auth Aj],
ZF [auth CD]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.249 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.34α = 94.69
b = 236.94β = 115.06
c = 249.71γ = 114.96
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-3000data reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2017-11-22
    Changes: Refinement description