[English] 日本語
Yorodumi
- EMDB-45442: Fusobacterium nucleatum BamA-Fab 9 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45442
TitleFusobacterium nucleatum BamA-Fab 9 complex
Map data
Sample
  • Complex: FnBamA-Fab9 complex
    • Protein or peptide: POTRA domain-containing protein
    • Protein or peptide: Fab 9 heavy chain
    • Protein or peptide: Fab 9 light chain
Keywordsproteomics / protein folding / membrane protein / structural biology
Function / homologyPOTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / cell outer membrane / POTRA domain-containing protein
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsOverly Cottom C / Noinaj N
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127884 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127896 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI127793 United States
CitationJournal: Structure / Year: 2025
Title: Characterization of the OMP biogenesis machinery in Fusobacterium nucleatum.
Authors: Claire Overly Cottom / Eva Heinz / Satchal Erramilli / Anthony Kossiakoff / Daniel J Slade / Nicholas Noinaj /
Abstract: F. nucleatum is a Gram-negative bacteria that causes oral infections and is linked to colorectal cancer. Pathogenicity relies on a type of β-barrel outer membrane protein (OMP) called an ...F. nucleatum is a Gram-negative bacteria that causes oral infections and is linked to colorectal cancer. Pathogenicity relies on a type of β-barrel outer membrane protein (OMP) called an autotransporter. The biogenesis of OMPs is typically mediated by the barrel assembly machinery (BAM) complex. In this study, we investigate the evolution, composition, and structure of the OMP biogenesis machinery in F. nucleatum. Our bioinformatics and proteomics analyses indicate that OMP biogenesis in F. nucleatum is mediated solely by the core component BamA. The structure of FnBamA highlights distinct features, including four POTRA domains and a C-terminal 16-stranded β-barrel domain observed as an inverted dimer. FnBamA represents the original composition of the assembly machinery, and a duplication event that resulted in BamA and TamA occurred after the split of other lineages, including the Proteobacteria, from the Fusobacteria. FnBamA, therefore, likely serves a singular role in the biogenesis of all OMPs.
History
DepositionJun 21, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45442.png

Downloads & links

-
Map

FileDownload / File: emd_45442.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0307
Minimum - Maximum-1.035032 - 1.2530943
Average (Standard dev.)0.00028107443 (±0.016389368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_45442_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_45442_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_45442_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FnBamA-Fab9 complex

EntireName: FnBamA-Fab9 complex
Components
  • Complex: FnBamA-Fab9 complex
    • Protein or peptide: POTRA domain-containing protein
    • Protein or peptide: Fab 9 heavy chain
    • Protein or peptide: Fab 9 light chain

-
Supramolecule #1: FnBamA-Fab9 complex

SupramoleculeName: FnBamA-Fab9 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Fusobacterium nucleatum (bacteria) / Strain: ATCC 23726
Molecular weightTheoretical: 121 kDa/nm

-
Macromolecule #1: POTRA domain-containing protein

MacromoleculeName: POTRA domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 75.980375 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LPIKSVEVVN NQQVPASLIK NTLKLKEGAK FSTEALLADF NALKETGYFE DVILQPVSYD GGVRIVVDVV EKENVVDLLK EKGVAINTL REDTDKSIVL SSVKFTGNKR VTTSELLDIT QLKAGEYFSR SRVEDAQRRL LATGKFSEVR PDAQVANGKM A LSFEVVEN ...String:
LPIKSVEVVN NQQVPASLIK NTLKLKEGAK FSTEALLADF NALKETGYFE DVILQPVSYD GGVRIVVDVV EKENVVDLLK EKGVAINTL REDTDKSIVL SSVKFTGNKR VTTSELLDIT QLKAGEYFSR SRVEDAQRRL LATGKFSEVR PDAQVANGKM A LSFEVVEN PIVKSVIITG NNTIPTSTIM SELTTKPGSV QNYNNLREDR DKILGLYQAQ GYTLVNITDM STDENGTLHI SI VEGIVRR IEVKKMVTKQ KGNRRTPNDD VLKTKDYVID REIEIQPGKI FNVKEYDATV DNLMRLGIFK NVKYEARSIP GDP EGIDLI LLIDEDRTAE LQGGVAYGSE TGFLGTLSLK DSNWRGKNQQ FGFTFEKSNK NYTGFALDFY DPWIKDTDRV SWGW GAYRT SYGDEDSILF HEIDTIGFRT NIGKGLGKNF TLSLGTKVEY IKEKHEDGKL RQANNGKWYY KEKNKWREIE GVDDK YWLW SIYPYISYDT RNNYLNPTSG FYGKFQVEAG HAGGYKSGNF GNATLELRTY HKGLFKNNIF AYKVVGGVAT NNTKES QKF WVGGGNSLRG YDGGFFKGSQ KLVATIENRT QLNDIIGLVV FADAGRAWKQ NGRDPSYTRD NSRFGHNIGT TAGVGIR LN TPIGPLRFDF GWPVGNKMDD DGMKFYFNMG QSF

UniProtKB: POTRA domain-containing protein

-
Macromolecule #2: Fab 9 heavy chain

MacromoleculeName: Fab 9 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 24.276992 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFNVY SSSIHWVRQA PGKGLEWVAS IYSYYGSTYY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARG YSSYWLKSHQ WPYGFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFNVY SSSIHWVRQA PGKGLEWVAS IYSYYGSTYY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARG YSSYWLKSHQ WPYGFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEP

-
Macromolecule #3: Fab 9 light chain

MacromoleculeName: Fab 9 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.100695 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QMTQSPSSLS ASVGDRVTIT CRASQSVSSA VAWYQQKPGK APKLLIYSAS SLYSGVPSRF SGSRSGTDFT LTISSLQPED FATYYCQQF SQRLVTFGQG TKVEIKRTVA APSVFIFPPS DSQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE S VTEQDSKD ...String:
QMTQSPSSLS ASVGDRVTIT CRASQSVSSA VAWYQQKPGK APKLLIYSAS SLYSGVPSRF SGSRSGTDFT LTISSLQPED FATYYCQQF SQRLVTFGQG TKVEIKRTVA APSVFIFPPS DSQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE S VTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTris-ClTris buffer, pH 7.6
150.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE
DetailsThis sample was monodisperse

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168664
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