8TU7 | pdb_00008tu7

Cryo-EM structure of Apoferritin collected by EPU on Glacios at 2.5 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb8TU7/pdb
EM Map EMD-41618: EMDB EMDataResource

Classification: METAL BINDING PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-15 Released: 2024-12-18
Deposition Author(s): Jia, L., Ruben, E.A., Olsen, S.K., Wasmuth, E.V.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8TU7

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of Apoferritin collected by EPU on Glacios at 2.5 Angstrom resolution

Jia, L., Ruben, E.A., Olsen, S.K., Wasmuth, E.V.

To be published.

Macromolecule Content

Total Structure Weight: 508.25 kDa
Atom Count: 33,846
Modeled Residue Count: 4,128
Deposited Residue Count: 4,368
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain	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	182	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 (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AB [auth W] SDF format, chain DA [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 PA [auth M] SDF format, chain QA [auth N] SDF format, chain SA [auth P] SDF format, chain XA [auth T] SDF format, chain YA [auth U] SDF format, chain ZA [auth V] SDF format, chain Z [auth A] SDF format, chain WA [auth S] SDF format, chain VA [auth R] SDF format, chain UA [auth Q] SDF format, chain RA [auth O] SDF format, chain OA [auth L] SDF format, chain NA [auth K] SDF format, chain MA [auth J] SDF format, chain LA [auth I] SDF format, chain BB [auth X] SDF format, chain BA [auth B] MOL2 format, chain AB [auth W] MOL2 format, chain DA [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 PA [auth M] MOL2 format, chain QA [auth N] MOL2 format, chain SA [auth P] MOL2 format, chain XA [auth T] MOL2 format, chain YA [auth U] MOL2 format, chain ZA [auth V] MOL2 format, chain Z [auth A] MOL2 format, chain WA [auth S] MOL2 format, chain VA [auth R] MOL2 format, chain UA [auth Q] MOL2 format, chain RA [auth O] MOL2 format, chain OA [auth L] MOL2 format, chain NA [auth K] MOL2 format, chain MA [auth J] MOL2 format, chain LA [auth I] MOL2 format, chain BB [auth X] MOL2 format, chain BA [auth B] mmCIF format, chain AB [auth W] mmCIF format, chain DA [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 PA [auth M] mmCIF format, chain QA [auth N] mmCIF format, chain SA [auth P] mmCIF format, chain XA [auth T] mmCIF format, chain YA [auth U] mmCIF format, chain ZA [auth V] mmCIF format, chain Z [auth A] mmCIF format, chain WA [auth S] mmCIF format, chain VA [auth R] mmCIF format, chain UA [auth Q] mmCIF format, chain RA [auth O] mmCIF format, chain OA [auth L] mmCIF format, chain NA [auth K] mmCIF format, chain MA [auth J] mmCIF format, chain LA [auth I] mmCIF format, chain BB [auth X] mmCIF format, chain BA [auth B]	AB [auth W] BA [auth B] BB [auth X] DA [auth C] FA [auth D] AB [auth W], BA [auth B], BB [auth X], DA [auth C], FA [auth D], GA [auth E], HA [auth F], IA [auth G], JA [auth H], LA [auth I], MA [auth J], NA [auth K], OA [auth L], PA [auth M], QA [auth N], RA [auth O], SA [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 AB [auth W] Focus chain BA [auth B] Focus chain BB [auth X] Focus chain DA [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 LA [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 SA [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 AB [auth W] Focus chain BA [auth B] Focus chain BB [auth X] Focus chain DA [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 LA [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 SA [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 (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CA [auth C] SDF format, chain EA [auth D] SDF format, chain KA [auth I] SDF format, chain TA [auth Q] SDF format, chain Y [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain KA [auth I] MOL2 format, chain TA [auth Q] MOL2 format, chain Y [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain KA [auth I] mmCIF format, chain TA [auth Q] mmCIF format, chain Y [auth A]	AA [auth B] CA [auth C] EA [auth D] KA [auth I] TA [auth Q] AA [auth B], CA [auth C], EA [auth D], KA [auth I], TA [auth Q], Y [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain CA [auth C] Focus chain EA [auth D] Focus chain KA [auth I] Focus chain TA [auth Q] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth C] Focus chain EA [auth D] Focus chain KA [auth I] Focus chain TA [auth Q] Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-12-18
Type: Initial release
Version 1.1: 2025-06-04
Changes: Data collection

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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.