9N5A | pdb_00009n5a

CryoEM structure of Azotobacter vinelandii bacterioferritin

PDB DOI: https://doi.org/10.2210/pdb9N5A/pdb
EM Map EMD-48919: EMDB EMDataResource

Classification: METAL BINDING PROTEIN
Organism(s): Azotobacter vinelandii DJ
Mutation(s): No

Deposited: 2025-02-03 Released: 2025-07-16
Deposition Author(s): Warmack, R.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.96 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes.

Shen, Y., Maggiolo, A.O., Zhang, T., Warmack, R.A.

(2025) Structure 33: 1484

PubMed: 40664216 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.str.2025.06.007
Primary Citation of Related Structures:
9N4V, 9N4W, 9N4X, 9N4Y, 9N59, 9N5A, 9NSV

PubMed Abstract:
Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry and machine learning, they promise to facilitate the visual exploration of proteomes. Leveraging visual proteomics, we interrogate structures isolated from a complex cellular milieu by cryoEM to identify and classify molecular structures and complexes de novo. By comparing three automated model building programs, CryoID, DeepTracer, and ModelAngelo, we determine the identity of six distinct oligomeric protein complexes from partially purified extracts of the nitrogen-fixing bacterium Azotobacter vinelandii using both anaerobic and aerobic cryoEM, including two original oligomeric structures. Overall, by allowing the study of near-native oligomeric protein states, cryoEM-enabled visual proteomics reveals unique structures that correspond to relevant species observed in situ.

Organizational Affiliation

Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA 91125, USA.

Macromolecule Content

Total Structure Weight: 439.36 kDa
Atom Count: 30,804
Modeled Residue Count: 3,720
Deposited Residue Count: 3,720
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	155	Azotobacter vinelandii DJ	Mutation(s): 0 EC: 1.16.3.1
UniProt
Find proteins for P22759 (Azotobacter vinelandii) Explore P22759 Go to UniProtKB: P22759
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22759
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 AA [auth E] SDF format, chain BA [auth H] SDF format, chain CA [auth I] SDF format, chain DA [auth L] SDF format, chain EA [auth M] SDF format, chain FA [auth P] SDF format, chain GA [auth Q] SDF format, chain HA [auth T] SDF format, chain IA [auth U] SDF format, chain JA [auth X] SDF format, chain Y [auth A] SDF format, chain Z [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth L] MOL2 format, chain EA [auth M] MOL2 format, chain FA [auth P] MOL2 format, chain GA [auth Q] MOL2 format, chain HA [auth T] MOL2 format, chain IA [auth U] MOL2 format, chain JA [auth X] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth L] mmCIF format, chain EA [auth M] mmCIF format, chain FA [auth P] mmCIF format, chain GA [auth Q] mmCIF format, chain HA [auth T] mmCIF format, chain IA [auth U] mmCIF format, chain JA [auth X] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth D]	AA [auth E] BA [auth H] CA [auth I] DA [auth L] EA [auth M] AA [auth E], BA [auth H], CA [auth I], DA [auth L], EA [auth M], FA [auth P], GA [auth Q], HA [auth T], IA [auth U], JA [auth X], Y [auth A], Z [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth E] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth L] Focus chain EA [auth M] Focus chain FA [auth P] Focus chain GA [auth Q] Focus chain HA [auth T] Focus chain IA [auth U] Focus chain JA [auth X] Focus chain Y [auth A] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth L] Focus chain EA [auth M] Focus chain FA [auth P] Focus chain GA [auth Q] Focus chain HA [auth T] Focus chain IA [auth U] Focus chain JA [auth X] Focus chain Y [auth A] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.96 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Warmack, R.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM143836
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM152765