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- PDB-9ome: CryoEM structure of FPM13 -

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Basic information

Entry
Database: PDB / ID: 9ome
TitleCryoEM structure of FPM13
ComponentsLipoprotein
KeywordsMETAL BINDING PROTEIN / Francisella / periplasmic protein / metal-binding protein
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein
Function and homology information
Biological speciesFrancisella (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu, X. / Zhou, Z.H. / Clemens, D.L. / Lee, B.Y. / Horwitz, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI151055 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
CitationJournal: PLoS Pathog / Year: 2026
Title: Discovery and cryoEM structure of FPM13, a periplasmic metalloprotein unique to Francisella.
Authors: Daniel L Clemens / Bai-Yu Lee / Xiaoyu Liu / Z Hong Zhou / Marcus A Horwitz /
Abstract: We report the identification and cryoEM structure of the Francisella protein FTN_1118, a previously uncharacterized 13 kDa periplasmic protein unique to the Francisella genus. The protein was ...We report the identification and cryoEM structure of the Francisella protein FTN_1118, a previously uncharacterized 13 kDa periplasmic protein unique to the Francisella genus. The protein was serendipitously discovered during purification of Francisella type VI secretion system (T6SS) effector proteins and is hereby designated as FPM13 (Francisella Periplasmic Metalloprotein, 13 kDa) based on its cellular and biochemical properties. Identified by the cryoID approach based on our cryoEM density map, FPM13 exists naturally as a cylindrical 18-mer complex with 9-fold dihedral symmetry, formed by stacking two donut-shaped nonamers head-to-head. Measuring ~8 nm in height and outer diameter with a 3.5 nm central channel, the complex features a double-layered wall comprising an inner β-sheet core and an outer α-helical shell. Each FPM13 monomer adopts a compact fold comprising an N-terminus β-strand, an α-helix and two additional β strands at the C-terminus. Inter-ring loop interactions, hydrophobic contacts, and electrostatic interactions between adjacent subunits stabilize the assembly. Biochemical analyses, including APEX-biotinylation and Triton X-114 phase partitioning, confirmed FPM13 as a soluble periplasmic protein. Inductively coupled plasma mass spectrometry (ICP-MS) revealed FPM13 binds iron, copper, and zinc, with alanine substitution of predicted metal-binding cysteine and histidine residues abolishing this capability. Biochemical assays further revealed that wild-type FPM13 catalyzes disulfide bond formation and rescues alkaline phosphatase from reductive inactivation, indicating a role in maintaining periplasmic disulfide bonds. The metal-binding disruption mutant loses this oxidation activity. Deletion of FPM13 in Francisella novicida caused no growth defects in vitro, in macrophages, or in mice under tested conditions, suggesting functional redundancy may compensate for its absence. This study unveils a novel metalloprotein and demonstrates the power of cryoID in identifying uncharacterized proteins directly from structural data, offering new insights into Francisella biology.
History
DepositionMay 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein
B: Lipoprotein
C: Lipoprotein
D: Lipoprotein
E: Lipoprotein
F: Lipoprotein
G: Lipoprotein
H: Lipoprotein
I: Lipoprotein
J: Lipoprotein
K: Lipoprotein
L: Lipoprotein
M: Lipoprotein
N: Lipoprotein
O: Lipoprotein
P: Lipoprotein
Q: Lipoprotein
R: Lipoprotein


Theoretical massNumber of molelcules
Total (without water)234,85918
Polymers234,85918
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Lipoprotein


Mass: 13047.735 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Francisella (bacteria) / References: UniProt: A0Q6Y9
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: FPM13 complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Francisella tularensis subsp. novicida (bacteria)
Source (recombinant)Organism: Francisella tularensis subsp. novicida (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1503607 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310800
ELECTRON MICROSCOPYf_angle_d0.57214472
ELECTRON MICROSCOPYf_dihedral_angle_d4.5931368
ELECTRON MICROSCOPYf_chiral_restr0.0481512
ELECTRON MICROSCOPYf_plane_restr0.0031854

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