9CZ8 | pdb_00009cz8

Structure of thioferritin exhibiting iron mineral nucleation, from Pyrococcus furiosis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of thioferritin from Pyrococcus furiosis.

Gauvin, C.C.Waghwani, H.K.Tokmina-Lukaszewska, M.Bothner, B.Douglas, T.Lawrence, C.M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA protection during starvation protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
170Pyrococcus furiosusMutation(s): 0 
Gene Names: dpsPF1193
EC: 1.16
UniProt
Find proteins for Q8U1L3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U1L3 
Go to UniProtKB:  Q8U1L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U1L3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth D]
AD [auth I]
AE [auth K]
BA [auth B]
AA [auth B],
AB [auth D],
AD [auth I],
AE [auth K],
BA [auth B],
BD [auth I],
CA [auth B],
CC [auth G],
CD [auth I],
CE [auth K],
DB [auth D],
DC [auth G],
EC [auth G],
ED [auth I],
FA [auth B],
FC [auth G],
GB [auth D],
GC [auth G],
GE [auth K],
HA [auth B],
IB [auth E],
ID [auth I],
IE [auth L],
JB [auth E],
JC [auth G],
JE [auth L],
KA [auth C],
KB [auth E],
KD [auth J],
KE [auth L],
LA [auth C],
LD [auth J],
M [auth A],
MA [auth C],
MB [auth E],
MD [auth J],
N [auth A],
NC [auth G],
ND [auth J],
NE [auth L],
O [auth A],
OA [auth C],
PB [auth E],
PD [auth J],
PE [auth L],
Q [auth A],
QA [auth C],
QC [auth H],
RC [auth H],
RD [auth J],
SB [auth F],
SC [auth H],
TB [auth F],
TC [auth H],
U [auth A],
UA [auth D],
UB [auth F],
UD [auth J],
VA [auth D],
W [auth A],
WA [auth D],
WB [auth F],
WC [auth H],
Y [auth A],
YA [auth D],
YD [auth K],
ZB [auth F],
ZD [auth K]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
O (Subject of Investigation/LOI)
Query on O

Download Ideal Coordinates CCD File 
AC [auth F]
BB [auth D]
BC [auth F]
BE [auth K]
CB [auth D]
AC [auth F],
BB [auth D],
BC [auth F],
BE [auth K],
CB [auth D],
DA [auth B],
DD [auth I],
DE [auth K],
EA [auth B],
EB [auth D],
EE [auth K],
FB [auth D],
FD [auth I],
FE [auth K],
GA [auth B],
GD [auth I],
HB [auth D],
HC [auth G],
HD [auth I],
HE [auth K],
IA [auth B],
IC [auth G],
JA [auth B],
JD [auth I],
KC [auth G],
LB [auth E],
LC [auth G],
LE [auth L],
MC [auth G],
ME [auth L],
NA [auth C],
NB [auth E],
OB [auth E],
OC [auth G],
OD [auth J],
OE [auth L],
P [auth A],
PA [auth C],
PC [auth G],
QB [auth E],
QD [auth J],
QE [auth L],
R [auth A],
RA [auth C],
RB [auth E],
RE [auth L],
S [auth A],
SA [auth C],
SD [auth J],
T [auth A],
TA [auth C],
TD [auth J],
UC [auth H],
V [auth A],
VB [auth F],
VC [auth H],
VD [auth J],
WD [auth J],
X [auth A],
XA [auth D],
XB [auth F],
XC [auth H],
XD [auth J],
YB [auth F],
YC [auth H],
Z [auth A],
ZA [auth D],
ZC [auth H]
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.5
MODEL REFINEMENTPHENIX1.21

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDBI-1828765

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release