9H1U | pdb_00009h1u

Cryo-EM structure of Heterooligomeric Bacterioferritin

PDB DOI: https://doi.org/10.2210/pdb9H1U/pdb
EM Map EMD-51772: EMDB EMDataResource

Classification: METAL BINDING PROTEIN
Organism(s): Magnetospirillum gryphiswaldense MSR-1
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-10-10 Released: 2025-10-29
Deposition Author(s): Stein, D., Zalk, R., Shahar, A., Zarivach, R., Frank, G.A.
Funding Organization(s): Israel Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.86 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

THE NEGATIVE DESIGN PRINCIPLES OF HETERO-OLIGOMERIC FERRITIN REVEALED BY CRYO-EM AND GRAPH-THEORY ANALYSIS

Stein, D., Jartoux, B., Dror, S., Koubkova-Yu, T.C.T., Zalk, R., Shahar, A., Uebe, R., Zarivach, R., Frank, A.G.

To be published.

Macromolecule Content

Total Structure Weight: 425.3 kDa
Atom Count: 29,095
Modeled Residue Count: 3,751
Deposited Residue Count: 3,792
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	A, B, C, D, E A, B, C, D, E, F, G, H	158	Magnetospirillum gryphiswaldense MSR-1	Mutation(s): 0 Gene Names: bfr, MGMSRv2__3703
UniProt
Find proteins for V6F8F5 (Magnetospirillum gryphiswaldense (strain DSM 6361 / JCM 21280 / NBRC 15271 / MSR-1)) Explore V6F8F5 Go to UniProtKB: V6F8F5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V6F8F5
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	I, J, K, L	158	Magnetospirillum gryphiswaldense MSR-1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	M, N, O, P, Q M, N, O, P, Q, R, S, T, U, V, W, X	158	Magnetospirillum gryphiswaldense MSR-1	Mutation(s): 0 Gene Names: MGR_0532
UniProt
Find proteins for Q6NE81 (Magnetospirillum gryphiswaldense) Explore Q6NE81 Go to UniProtKB: Q6NE81
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NE81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth B] SDF format, chain BA [auth G] SDF format, chain AA [auth E] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth E]	AA [auth E], BA [auth G], Y [auth B], Z [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth E] Focus chain BA [auth G] Focus chain Y [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth G] Focus chain Y [auth B] Focus chain Z [auth C]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain RA [auth X] SDF format, chain QA [auth X] SDF format, chain PA [auth W] SDF format, chain OA [auth W] SDF format, chain NA [auth V] SDF format, chain MA [auth V] SDF format, chain LA [auth U] SDF format, chain KA [auth T] SDF format, chain JA [auth T] SDF format, chain IA [auth R] SDF format, chain HA [auth Q] SDF format, chain GA [auth O] SDF format, chain FA [auth N] SDF format, chain EA [auth N] SDF format, chain DA [auth M] SDF format, chain CA [auth M] MOL2 format, chain RA [auth X] MOL2 format, chain QA [auth X] MOL2 format, chain PA [auth W] MOL2 format, chain OA [auth W] MOL2 format, chain NA [auth V] MOL2 format, chain MA [auth V] MOL2 format, chain LA [auth U] MOL2 format, chain KA [auth T] MOL2 format, chain JA [auth T] MOL2 format, chain IA [auth R] MOL2 format, chain HA [auth Q] MOL2 format, chain GA [auth O] MOL2 format, chain FA [auth N] MOL2 format, chain EA [auth N] MOL2 format, chain DA [auth M] MOL2 format, chain CA [auth M] mmCIF format, chain RA [auth X] mmCIF format, chain QA [auth X] mmCIF format, chain PA [auth W] mmCIF format, chain OA [auth W] mmCIF format, chain NA [auth V] mmCIF format, chain MA [auth V] mmCIF format, chain LA [auth U] mmCIF format, chain KA [auth T] mmCIF format, chain JA [auth T] mmCIF format, chain IA [auth R] mmCIF format, chain HA [auth Q] mmCIF format, chain GA [auth O] mmCIF format, chain FA [auth N] mmCIF format, chain EA [auth N] mmCIF format, chain DA [auth M] mmCIF format, chain CA [auth M]	CA [auth M] DA [auth M] EA [auth N] FA [auth N] GA [auth O] CA [auth M], DA [auth M], EA [auth N], FA [auth N], GA [auth O], HA [auth Q], IA [auth R], JA [auth T], KA [auth T], LA [auth U], MA [auth V], NA [auth V], OA [auth W], PA [auth W], QA [auth X], RA [auth X]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain CA [auth M] Focus chain DA [auth M] Focus chain EA [auth N] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain HA [auth Q] Focus chain IA [auth R] Focus chain JA [auth T] Focus chain KA [auth T] Focus chain LA [auth U] Focus chain MA [auth V] Focus chain NA [auth V] Focus chain OA [auth W] Focus chain PA [auth W] Focus chain QA [auth X] Focus chain RA [auth X] Interactions & Density Focus chain CA [auth M] Focus chain DA [auth M] Focus chain EA [auth N] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain HA [auth Q] Focus chain IA [auth R] Focus chain JA [auth T] Focus chain KA [auth T] Focus chain LA [auth U] Focus chain MA [auth V] Focus chain NA [auth V] Focus chain OA [auth W] Focus chain PA [auth W] Focus chain QA [auth X] Focus chain RA [auth X]