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- PDB-9n5a: CryoEM structure of Azotobacter vinelandii bacterioferritin -

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Basic information

Entry
Database: PDB / ID: 9n5a
TitleCryoEM structure of Azotobacter vinelandii bacterioferritin
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / Metal storage
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / heme binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Bacterioferritin
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsWarmack, R.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143836 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM152765 United States
CitationJournal: To Be Published
Title: CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes
Authors: Warmack, R.A.
History
DepositionFeb 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
M: Bacterioferritin
N: Bacterioferritin
O: Bacterioferritin
P: Bacterioferritin
Q: Bacterioferritin
R: Bacterioferritin
S: Bacterioferritin
T: Bacterioferritin
U: Bacterioferritin
V: Bacterioferritin
W: Bacterioferritin
X: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,36436
Polymers431,96624
Non-polymers7,39812
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Bacterioferritin / BFR / Cytochrome b-557.5


Mass: 17998.574 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ / References: UniProt: P22759, ferroxidase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacterioferritin / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -2500 nm / Nominal defocus min: -800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15105 / Symmetry type: POINT
RefinementHighest resolution: 2.96 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00331368
ELECTRON MICROSCOPYf_angle_d0.64442360
ELECTRON MICROSCOPYf_dihedral_angle_d6.6874032
ELECTRON MICROSCOPYf_chiral_restr0.0344560
ELECTRON MICROSCOPYf_plane_restr0.0025400

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