23WJ | pdb_000023wj

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

PDB DOI: https://doi.org/10.2210/pdb23WJ/pdb
EM Map EMD-67082: EMDB EMDataResource

Classification: RECOMBINATION
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-02-23 Released: 2026-04-22
Deposition Author(s): Yanagisawa, H., Eisenstein, F., Miyata, T., Kinoshita, M., Kikkawa, M., Namba, K., Makino, F.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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

DOI: https://doi.org/10.3934/biophy.2026008

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:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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	172	Mus musculus	Mutation(s): 0 Gene Names: Fth1, Fth 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09528
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth W] SDF format, chain BB [auth X] SDF format, chain CA [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth F] SDF format, chain IA [auth G] SDF format, chain JA [auth H] SDF format, chain KA [auth I] SDF format, chain MA [auth J] SDF format, chain NA [auth K] SDF format, chain OA [auth L] SDF format, chain PA [auth M] SDF format, chain QA [auth N] SDF format, chain RA [auth O] SDF format, chain TA [auth P] SDF format, chain UA [auth Q] SDF format, chain VA [auth R] SDF format, chain WA [auth S] SDF format, chain XA [auth T] SDF format, chain YA [auth U] SDF format, chain Z [auth A] SDF format, chain ZA [auth V] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth W] MOL2 format, chain BB [auth X] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain MA [auth J] MOL2 format, chain NA [auth K] MOL2 format, chain OA [auth L] MOL2 format, chain PA [auth M] MOL2 format, chain QA [auth N] MOL2 format, chain RA [auth O] MOL2 format, chain TA [auth P] MOL2 format, chain UA [auth Q] MOL2 format, chain VA [auth R] MOL2 format, chain WA [auth S] MOL2 format, chain XA [auth T] MOL2 format, chain YA [auth U] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth V] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth W] mmCIF format, chain BB [auth X] mmCIF format, chain CA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain KA [auth I] mmCIF format, chain MA [auth J] mmCIF format, chain NA [auth K] mmCIF format, chain OA [auth L] mmCIF format, chain PA [auth M] mmCIF format, chain QA [auth N] mmCIF format, chain RA [auth O] mmCIF format, chain TA [auth P] mmCIF format, chain UA [auth Q] mmCIF format, chain VA [auth R] mmCIF format, chain WA [auth S] mmCIF format, chain XA [auth T] mmCIF format, chain YA [auth U] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth V]	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		Interactions Focus chain AA [auth B] Focus chain AB [auth W] Focus chain BB [auth X] Focus chain CA [auth C] Focus chain FA [auth D] Focus chain GA [auth E] Focus chain HA [auth F] Focus chain IA [auth G] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain NA [auth K] Focus chain OA [auth L] Focus chain PA [auth M] Focus chain QA [auth N] Focus chain RA [auth O] Focus chain TA [auth P] Focus chain UA [auth Q] Focus chain VA [auth R] Focus chain WA [auth S] Focus chain XA [auth T] Focus chain YA [auth U] Focus chain Z [auth A] Focus chain ZA [auth V] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth W] Focus chain BB [auth X] Focus chain CA [auth C] Focus chain FA [auth D] Focus chain GA [auth E] Focus chain HA [auth F] Focus chain IA [auth G] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain NA [auth K] Focus chain OA [auth L] Focus chain PA [auth M] Focus chain QA [auth N] Focus chain RA [auth O] Focus chain TA [auth P] Focus chain UA [auth Q] Focus chain VA [auth R] Focus chain WA [auth S] Focus chain XA [auth T] Focus chain YA [auth U] Focus chain Z [auth A] Focus chain ZA [auth V]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain DA [auth C] SDF format, chain EA [auth D] SDF format, chain LA [auth I] SDF format, chain SA [auth O] SDF format, chain Y [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain LA [auth I] MOL2 format, chain SA [auth O] MOL2 format, chain Y [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain LA [auth I] mmCIF format, chain SA [auth O] mmCIF format, chain Y [auth A]	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		Interactions Focus chain BA [auth B] Focus chain DA [auth C] Focus chain EA [auth D] Focus chain LA [auth I] Focus chain SA [auth O] Focus chain Y [auth A] Interactions & Density Focus chain BA [auth B] Focus chain DA [auth C] Focus chain EA [auth D] Focus chain LA [auth I] Focus chain SA [auth O] Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	5

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP22am121003
Japan Agency for Medical Research and Development (AMED)	Japan	JP17pc0101020

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.