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- EMDB-53048: Extracellular domain of the Fap2 autotransporter adhesin from Fus... -

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Basic information

Entry
Database: EMDB / ID: EMD-53048
TitleExtracellular domain of the Fap2 autotransporter adhesin from Fusobacterium nucleatum ATCC23726
Map dataMain map, sharpened using deepEMhancer (tight model)
Sample
  • Complex: Fap2 extracellular domain from F. nucleatum ATCC23726, monomer
    • Protein or peptide: Fap2 extracellular domain from F. nucleatum ATCC23726
KeywordsType V secretion system / autotransporter / colorectal cancer / bacterial adhesion / CELL ADHESION
Biological speciesFusobacterium nucleatum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsSchoepf F / Marongiu GL / Milaj K / Sprink T / Kikhney J / Moter A / Roderer D
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)548509121 Germany
CitationJournal: To Be Published
Title: Structural basis of Fusobacterium nucleatum adhesin Fap2 interaction with receptors on cancer and immune cells
Authors: Schoepf F / Marongiu GL / Milaj K / Sprink T / Kikhney J / Moter A / Roderer D
History
DepositionMar 7, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53048.png

Downloads & links

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Map

FileDownload / File: emd_53048.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, sharpened using deepEMhancer (tight model)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 700 pix.
= 742. Å		1.06 Å/pix.
x 700 pix.
= 742. Å		1.06 Å/pix.
x 700 pix.
= 742. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.046
Minimum - Maximum-0.0017550894 - 1.8966228
Average (Standard dev.)0.000059989023 (±0.00574848)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 741.99994 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53048_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-sharpened main map

Fileemd_53048_additional_1.map
AnnotationNon-sharpened main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53048_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53048_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Fap2 extracellular domain from F. nucleatum ATCC23726, monomer

EntireName: Fap2 extracellular domain from F. nucleatum ATCC23726, monomer
Components
  • Complex: Fap2 extracellular domain from F. nucleatum ATCC23726, monomer
    • Protein or peptide: Fap2 extracellular domain from F. nucleatum ATCC23726

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Supramolecule #1: Fap2 extracellular domain from F. nucleatum ATCC23726, monomer

SupramoleculeName: Fap2 extracellular domain from F. nucleatum ATCC23726, monomer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: Fap2 extracellular domain from F. nucleatum ATCC23726

MacromoleculeName: Fap2 extracellular domain from F. nucleatum ATCC23726 / type: protein_or_peptide / ID: 1
Details: Fap2 (1-3271) with C-terminal histag and TEV cleavage site
Enantiomer: LEVO
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EEVNLENSQV ATREELKTSV GNVQTKLNIL RNENKEKIKN LRLELIQLME QGDQVVKSPW SSWQFGMNYF YENWRSTYKG SGDKSEKYVF NGIYTRGNWK VRNAMDMAEN QRVGGRPLTP GNDSLNSWKN ASNSSGGGVT IDKDTSIGSS TNGNKSWGLV DLRDLREPTN ...String:
EEVNLENSQV ATREELKTSV GNVQTKLNIL RNENKEKIKN LRLELIQLME QGDQVVKSPW SSWQFGMNYF YENWRSTYKG SGDKSEKYVF NGIYTRGNWK VRNAMDMAEN QRVGGRPLTP GNDSLNSWKN ASNSSGGGVT IDKDTSIGSS TNGNKSWGLV DLRDLREPTN EVEILAHISP KEVTKQVISL NITEPTVQTL EAPDVNPQVN EPLPAPVIEL PEVETVTINP LSINAPSAPT APSAPTINIA ITAPSAPVPP TINVVPASPS TPSAPTINIG IQPPSITPLS ITTPDSVDAP NVVSPQIKPV DFTVDPGGDS NVYSSEKHNS HQGWKATWDK TINVTELTNR NYVSLTRDVV DSTIPDDQVI NVTKPNNRAM VVDEVRKNGI KVDFKGTINL QRSQNVGIDL QGTHQGSIST PLIANIYNSG KIIGNAKYGS TANKEQIAFG FNNADGSNNT TMTNMVNKGE ITLNAPSSAG IQLKPEDPHD WQPGAPNYWN AAPLQIGNKT PNKIKGRVLM KADNQKDINL NGSGSFGMVT VFNEGVPKRL FAPSYVANYE NLRSERTYDG ERVLPGGEIG RSALSDSKYT SGVYNTGNIN INGDSSIGVG LLQEIQEVKL AGNINIGTKA VAQETDISNL PNAGSKTYDK NKVEEAVGVF AGVPTMPVKP GEKDTLINSS GARNTATSLV GTETVEINGN ISLGEHATQS IGALVGDTEI DLNKGQLTEN GVNKGSNVDR KLKRSGDITA KSNSVINVGG KKNYGFVVSN SAHSSKFGTT VDSLEYNVDK THHGKGINEG IINIIGDESV GFAMIKGGNS KSSGTISVKD NAENSIGFYG KEDSFTNSGT IEVTSAKKKN KAVVLDGTNA SNKINFTNTG NIYVNTSDNN NTNLDGNGNI GIYAQGNYKV EHNSGIVKAG KDVIAFYVKD STGEVNINAP IELANSSKGT TIGIYSDGNA KVKFGTGSKL KIGEKAVGLY SADPTKFNNT FKIESGKTLD VELGKNSTFG LLNGNNTVTN SPLLSKYLNN NTSDKINIVS FGEGASLFYA TSKAKAILDE DYKVTNGDAI STAVLVANNG ANVEIASGKK LETNTNAGLI AINGTVGFTS VAKNNGTLIS TRIDKGIGIY TSAANGENSG TITMQNKNAV GILGSKDSNL KNTGKIELEA VSSAGVYAED SNMINSGTTS EIIVNKETSV GIYAKETSIS SVSKNVKNEG KIEIKADGDG KSAGIYSKKE GGAKLTIENT GNIEVAQKAS AGIYAKNEST QANTQSEVTN SGLVKMSAEN SIGIMGEKSK ITNTGTGTKG IEIVEKKSAG ILVTNESAVI NSGRISLSNS SISASSDGLV GISVDGSSTG ENDASGEIKV DAAYSTGMLS SGGGITNAGK IALEKKESVG MYATNANVTN SGATPKGIFI KDEKSVGIYS KINSSSIANK TVTNSGTIDI AGTSKTGSAG IYSIIESGAT KKLSVVNNGN ITINQKKSVG IYAKNESSHA NTESDVTNSG KIEVKNEGSA GVLAEKYKVT NTGSGTNGII VSAKKSAGII GKLGSEIINS GIIKTEIATP TVATDGVVGI SLNNSKATNT SGGVITLDTD YSTGMYGEAN SQLTNEGNIT GTNKEYIVGM AGDSSTVTNK NIITLNGKKA TGIFGKNSST LLNETTGKIT TKEEESVGMY SSSSLKATNK GTIITEKKTS AGMLGDKANI ENDSSITTKE EMSAGMYVKN GTSKATNKGT VTTEKKTSAG ILAEIDEANG GTVSGLNETT GTITVSEETS AGMLGKVKSA VTASTAKLSL TNKKDININT KNSAGIMVVN ESTAVGKENV LAENTGIINL TSSSATNEKN IGILANKATG INTGNINVNS KESIGMLGQN ASSITNNKTI TLSGEKGIGM LSKDTSSIAD NNDTINVNGK ESLGMLGEDS GTVKNNKTIS VTAEKGVGIF VRDNGVGKGS GTGENTSTGT ITLENKEAVG IFAKNNGTSD SAKNSGTINL GKADGSTIKE SLIGMFAQAE AGKKANVKNT KDINVNTKKS VGIYAKNDAS NITDVDLENT GDININSKES AGVYAPKANI SKVGTITLKN SIDSNGSSAV YVSKGGKVAN TAGAKINLGT VNQNRVAYYV NGKDSALAGA DIGKITGYGV GVYLQGTSGD KATLDKNTSK LDYTLQGTGN GIIGLLLKGE TDIQSYTKGI KVGNTVAATS PSDKAKYAIG IYADAQGTAG TPYNITTPIT AGKSGVGIFA DKDSNINYTG NMEIGDGTTA GTGIFITKKI GATGGKVTLG TNTIKLKGTK GVVAIASEGT TFNGGNATIE LVGSNIQGVG VYAKKGSTVN IDHWTFNNNG NSAEEVRSEE GRVYINANKN LKPKMVLTHV INGETSIATG KTVTSVNDGS ITAKENIGLM AEGIKNHSMT WQEGNFEAVN HGIIDFSAAE KSTAMFINSA RAKNDGTIKV GKNSIGIYGF YNKDTRKYDG ASTNPDPNKL ELETTSNSKM SLGDASTGMY LTNAEKIENK GGQITSESGA TKNVGIYAVN GQDTKVSANN KILNMTTATN INLGNGSVGL YSKGQSNTVR NTVTNTGDIT VGDKITGSPS VAMYAENTNL TTNSKITVGK DGIAFYGKNS DITAKGSANF SNKGVLAYLE NSKFVSHLGN LGSTQNTMLY LKNSIAQLDG AGTKVDMDVA DGYTGAYIEG NSTLTGVKTI KLGQDSTGLF LKDANFVSNA ESITGTKDKA RGILATNSNL TNNSKIFLSG AESIGIYSNA NNTKSVVNNG ELTIAGKKTL GVFLKGSQSF ENKANINIAD SANSLEPTIG IYTAEGSSNI KHTSGTIDVG QKSIGIYSTT NSNVEMNGGK IHVKDQGVGI YKQNGKATIK GELDIDTHIA TTKDSEPTGV YAVNGTEIND QASKISIGAK SYGFILNNTD PNKTNIYTNT DAGTVSLGND SVFLYSNGKA NIINNRTINA NGASHLIAFY IKNGGNFTNN GTIDFSTGKG NIGIYAPGGK ATNKGRVYVG KTDDIDPMTG KVYSDVSKIV YGIGMAADNG GYIKNDGEIR IYNNKSIGMY GKGIGTTVEN TGKIYLDGSR ATATDKIQSM TGVYVDDGAK FINRGEIRTT DSYAGRDGKV NENVTGLVGV AVMNGSTLEN HGKILIDADN SYGVIIRGKR DSKGNVERYA VIKNYGEIKV RGKGTWGISW KDVSQAYIDE LQKQINDKIS SDPEGQALRA GSAHHHHHHH HSAGENLYFQ

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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

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris HCl, 200 mM NaCl, pH 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12663 / Average exposure time: 2.0 sec. / Average electron dose: 58.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 265956
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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