7DIE | pdb_00007die

Crystal structure of M. penetrans Ferritin

PDB DOI: https://doi.org/10.2210/pdb7DIE/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Malacoplasma penetrans HF-2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-11-19 Released: 2021-05-26
Deposition Author(s): Wang, w.m., Zhang, y., Wang, h.f.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.177 (Depositor), 0.178 (DCC)
R-Value Work:
0.153 (Depositor), 0.154 (DCC)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Ferritin with Atypical Ferroxidase Centers Takes B-Channels as the Pathway for Fe 2+ Uptake from Mycoplasma .

Wang, W., Zhang, Y., Zhao, G., Wang, H.

(2021) Inorg Chem 60: 7207-7216

PubMed: 33852289 Search on PubMed
DOI: https://doi.org/10.1021/acs.inorgchem.1c00265
Primary Citation Related Structures:
7DIE

PubMed Abstract:
Here, we present a 1.9 Å resolution crystal structure of Mycoplasma Penetrans ferritin, which reveals that its ferroxidase center is located on the inner surface of ferritin but not buried within the four-helix of each subunit. Such a ferroxidase center exhibits a lower iron oxidation activity as compared to the reported ferritin. More importantly, we found that Fe ²⁺ enters into the center via the rarely reported B-channels rather than the normal 3- or 4-fold channels. All these findings may provide the structural bases to explore the new iron oxidation mechanism adopted by this special ferritin, which is beneficial for understanding the relationship between the structure and function of ferritin.

Organizational Affiliation

Institute of Molecular Science, Shanxi University, Taiyuan 030006, China.

Macromolecule Content

Total Structure Weight: 125.99 kDa
Atom Count: 8,877
Modeled Residue Count: 984
Deposited Residue Count: 1,074
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A, B, C, D, E A, B, C, D, E, F	179	Malacoplasma penetrans HF-2	Mutation(s): 0 Gene Names: MYPE2930 EC: 1.16.3.2
UniProt
Find proteins for Q8EWB1 (Malacoplasma penetrans (strain HF-2)) Explore Q8EWB1 Go to UniProtKB: Q8EWB1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8EWB1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain PA [auth F] SDF format, chain P [auth B] SDF format, chain OA [auth F] SDF format, chain O [auth B] SDF format, chain NA [auth F] SDF format, chain N [auth A] SDF format, chain MA [auth F] SDF format, chain M [auth A] SDF format, chain LA [auth F] SDF format, chain L [auth A] SDF format, chain KA [auth F] SDF format, chain K [auth A] SDF format, chain JA [auth F] SDF format, chain J [auth A] SDF format, chain IA [auth F] SDF format, chain I [auth A] SDF format, chain HA [auth F] SDF format, chain H [auth A] SDF format, chain GA [auth E] SDF format, chain G [auth A] SDF format, chain FA [auth E] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain CA [auth E] SDF format, chain BA [auth E] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth E] CA [auth E] DA [auth E] EA [auth E] AA [auth D], BA [auth E], CA [auth E], DA [auth E], EA [auth E], FA [auth E], G [auth A], GA [auth E], H [auth A], HA [auth F], I [auth A], IA [auth F], J [auth A], JA [auth F], K [auth A], KA [auth F], L [auth A], LA [auth F], M [auth A], MA [auth F], N [auth A], NA [auth F], O [auth B], OA [auth F], P [auth B], PA [auth F], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth D], Z [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D]