[English] 日本語
Yorodumi
- EMDB-70611: CryoEM structure of FPM13 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70611
TitleCryoEM structure of FPM13
Map dataEM map
Sample
  • Complex: FPM13 complex
    • Protein or peptide: Lipoprotein
KeywordsFrancisella / periplasmic protein / metal-binding protein / METAL BINDING PROTEIN
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein
Function and homology information
Biological speciesFrancisella tularensis subsp. novicida (bacteria) / Francisella (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu X / Zhou ZH / Clemens DL / Lee BY / Horwitz MA / Horwitz M
Funding support United States, 2 items
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, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70611.png

Downloads & links

-
Map

FileDownload / File: emd_70611.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027
Minimum - Maximum-0.0947312 - 0.16107467
Average (Standard dev.)-0.00009516747 (±0.0035264373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map

Fileemd_70611_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map

Fileemd_70611_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FPM13 complex

EntireName: FPM13 complex
Components
  • Complex: FPM13 complex
    • Protein or peptide: Lipoprotein

-
Supramolecule #1: FPM13 complex

SupramoleculeName: FPM13 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Francisella tularensis subsp. novicida (bacteria)

-
Macromolecule #1: Lipoprotein

MacromoleculeName: Lipoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Francisella (bacteria)
Molecular weightTheoretical: 13.047735 KDa
SequenceString:
MFKKSFICIV FFLISGFALA CSHDSGKHFS FNLDIKVNGD KKELYIKKYK EIENYVKEFN DKNSTNYQIE RIEFSKSYQY ENVETALVS LVEPSSTSSN KDKCKYHNHD KN

UniProtKB: Lipoprotein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1503607
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more