[English] 日本語
Yorodumi
- EMDB-53052: Complex of Fap2 from Fusobacterium nucleatum with human TIGIT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53052
TitleComplex of Fap2 from Fusobacterium nucleatum with human TIGIT
Map dataNon-sharpened main map
Sample
  • Complex: Fap2 extracellular domain from F. nucleatum ATCC23726, 1:1 complex with human TIGIT (ECD in fusion with eGFP)
    • Protein or peptide: Fap2 extracellular domain
    • Protein or peptide: Fusion protein of human TIGIT with eGFP
KeywordsType V secretion system / autotransporter / colorectal cancer / bacterial adhesion / immune cell protein / CELL ADHESION
Biological speciesFusobacterium nucleatum (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 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: Nat Commun / Year: 2025
Title: Structural basis of Fusobacterium nucleatum adhesin Fap2 interaction with receptors on cancer and immune cells.
Authors: Felix Schöpf / Gian L Marongiu / Klaudia Milaj / Thiemo Sprink / Judith Kikhney / Annette Moter / Daniel Roderer /
Abstract: Fusobacterium nucleatum is overrepresented in the colon microbiome of colorectal cancer patients and has been associated with tumor growth enhancement and metastasis. A pivotal pathogenic factor, the ...Fusobacterium nucleatum is overrepresented in the colon microbiome of colorectal cancer patients and has been associated with tumor growth enhancement and metastasis. A pivotal pathogenic factor, the autotransporter adhesin Fap2, facilitates association to cancer and immune cells via the receptors Gal-GalNAc and TIGIT, respectively, leading to deactivation of immune cells. Mechanistic details of the Fap2/TIGIT interaction remain elusive as no structural data are available. Here, we report a system to recombinantly express functional Fap2 on the Escherichia coli surface, which interacts with Gal-GalNAc on cancer cells and with purified TIGIT with submicromolar affinity. Cryo-EM structures of Fap2, alone and in complex with TIGIT, show that the elongated ~50 nm long Fap2 extracellular region binds to TIGIT on its membrane-distal tip via an extension of a β-helix domain. Moreover, by combining structure predictions, cryo-EM, docking and molecular dynamics simulations, we identified a binding pit for Gal-GalNAc on the tip of Fap2.
History
DepositionMar 7, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53052.png

Downloads & links

-
Map

FileDownload / File: emd_53052.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-sharpened main map
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: 0.086
Minimum - Maximum-0.08693002 - 0.4671067
Average (Standard dev.)-0.00019739397 (±0.005979248)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_53052_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened main map

Fileemd_53052_additional_1.map
AnnotationSharpened main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_53052_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_53052_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Fap2 extracellular domain from F. nucleatum ATCC23726, 1:1 comple...

EntireName: Fap2 extracellular domain from F. nucleatum ATCC23726, 1:1 complex with human TIGIT (ECD in fusion with eGFP)
Components
  • Complex: Fap2 extracellular domain from F. nucleatum ATCC23726, 1:1 complex with human TIGIT (ECD in fusion with eGFP)
    • Protein or peptide: Fap2 extracellular domain
    • Protein or peptide: Fusion protein of human TIGIT with eGFP

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

SupramoleculeName: Fap2 extracellular domain from F. nucleatum ATCC23726, 1:1 complex with human TIGIT (ECD in fusion with eGFP)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 400 KDa

-
Macromolecule #1: Fap2 extracellular domain

MacromoleculeName: Fap2 extracellular domain / type: protein_or_peptide / ID: 1 / Details: Fap2 extracellular domain (42-3271) / 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

-
Macromolecule #2: Fusion protein of human TIGIT with eGFP

MacromoleculeName: Fusion protein of human TIGIT with eGFP / type: protein_or_peptide / ID: 2
Details: human TIGIT extracellular domain in fusion with eGFP
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRWCLLLIWA QGLRQAPLAS GMMTGTIETT GNISAEKGGS IILQCHLSST TAQVTQVNWE QQDQLLAICN ADLGWHISPS FKDRVAPGPG LGLTLQSLTV NDTGEYFCIY HTYPDGTYTG RIFLEVLESS VAEHGARFQI PLEVLFQGPG GSMSKGEELF TGVVPILVEL ...String:
MRWCLLLIWA QGLRQAPLAS GMMTGTIETT GNISAEKGGS IILQCHLSST TAQVTQVNWE QQDQLLAICN ADLGWHISPS FKDRVAPGPG LGLTLQSLTV NDTGEYFCIY HTYPDGTYTG RIFLEVLESS VAEHGARFQI PLEVLFQGPG GSMSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTLTYGV QCFSRYPDHM KQHDFFKSAM PEGYVQERTI FFKDDGNYKT RAEVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNYNSH NVYIMADKQK NGIKVNFKIR HNIEDGSVQL ADHYQQNTPI GDGPVLLPDN HYLSTQSALS KDPNEKRDHM VLLEFVTAAG ITHGMDELYK SGRMAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKTSN

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris HCl, 150 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
DetailsSample was applied three times

-
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: 15658 / Average exposure time: 2.0 sec. / Average electron dose: 44.6 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: 2.5 µm / Nominal defocus min: 1.0 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

+
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: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 45207
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

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

+
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