23WJ | pdb_000023wj

Subtomogram average of Apoferrtin (11x11) using CRYO ARM 300II


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation 3D Report Full Report

Validation slider image for 23WJ

This is version 1.0 of the entry. See complete history

Literature

Subtomogram averaging by cryo electron tomography using CRYO ARMTM 300 II for purified and cellular samples

Makino, F.Yanagisawa, H.Eisenstein, F.Miyata, T.Kinoshita, M.Kikkawa, M.Namba, K.

(2026) Aims Biophysics 13: 131-142

Macromolecule Content 

  • Total Structure Weight: 483.82 kDa 
  • Atom Count: 33,846 
  • Modeled Residue Count: 4,128 
  • Deposited Residue Count: 4,128 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferritin heavy chain, N-terminally processed
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
172Mus musculusMutation(s): 0 
Gene Names: Fth1Fth
EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P09528 (Mus musculus)
Explore P09528 
Go to UniProtKB:  P09528
IMPC:  MGI:95588
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09528
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth W]
BB [auth X]
CA [auth C]
FA [auth D]
AA [auth B],
AB [auth W],
BB [auth X],
CA [auth C],
FA [auth D],
GA [auth E],
HA [auth F],
IA [auth G],
JA [auth H],
KA [auth I],
MA [auth J],
NA [auth K],
OA [auth L],
PA [auth M],
QA [auth N],
RA [auth O],
TA [auth P],
UA [auth Q],
VA [auth R],
WA [auth S],
XA [auth T],
YA [auth U],
Z [auth A],
ZA [auth V]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
BA [auth B]
DA [auth C]
EA [auth D]
LA [auth I]
SA [auth O]
BA [auth B],
DA [auth C],
EA [auth D],
LA [auth I],
SA [auth O],
Y [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION5

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP22am121003
Japan Agency for Medical Research and Development (AMED)JapanJP17pc0101020

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-22
    Type: Initial release