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- EMDB-45442: Fusobacterium nucleatum BamA-Fab 9 complex -

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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: To Be Published
Title: Characterization of the OMP biogenesis machinery in Fusobacterium nucleatum
Authors: Overly Cottom C / Heinz E / Eramilli S / Slade DJ / Kossiakoff A / Noinaj N
History
DepositionJun 21, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45442.png

Downloads & links

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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 °

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Supplemental data

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Additional map: #1

Fileemd_45442_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45442_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45442_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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

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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

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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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

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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

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