[English] 日本語
Yorodumi
- EMDB-53049: Membrane-distal part of extracellular domain of the Fap2 autotran... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53049
TitleMembrane-distal part of extracellular domain of the Fap2 autotransporter adhesin from Fusobacterium nucleatum ATCC23726
Map dataMain map, sharpened with deepEMhancer
Sample
  • Complex: Fap2 extracellular domain from F. nucleatum ATCC23726, monomer
    • Protein or peptide: Outer membrane autotransporter barrel domain protein
KeywordsType V secretion system / autotransporter / colorectal cancer / bacterial adhesion / CELL ADHESION
Function / homology
Function and homology information


: / Autotransporter beta-domain / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Outer membrane autotransporter barrel domain protein
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 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

-
Structure visualization

Supplemental images

emd_53049.png

Downloads & links

-
Map

FileDownload / File: emd_53049.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, sharpened with deepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 384 pix.
= 407.04 Å		1.06 Å/pix.
x 384 pix.
= 407.04 Å		1.06 Å/pix.
x 384 pix.
= 407.04 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: 0.25
Minimum - Maximum-0.0013087961 - 1.460411
Average (Standard dev.)0.00061168964 (±0.016177451)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 407.03998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_53049_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Non-sharpened main map

Fileemd_53049_additional_1.map
AnnotationNon-sharpened main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_53049_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_53049_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, monomer

EntireName: Fap2 extracellular domain from F. nucleatum ATCC23726, monomer
Components
  • Complex: Fap2 extracellular domain from F. nucleatum ATCC23726, monomer
    • Protein or peptide: Outer membrane autotransporter barrel domain protein

-
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

-
Macromolecule #1: Outer membrane autotransporter barrel domain protein

MacromoleculeName: Outer membrane autotransporter barrel domain protein / type: protein_or_peptide / ID: 1
Details: Extracellular domain of F. nucleatum adhesin Fap2, membrane-distal part
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 340.269375 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EEVNLENSQV ATREELKTSV GNVQTKLNIL RNENKEKIKN LRLELIQLME QGDQVVKSPW SSWQFGMNYF YENWRSTYKG SGDKSEKYV FNGIYTRGNW KVRNAMDMAE NQRVGGRPLT PGNDSLNSWK NASNSSGGGV TIDKDTSIGS STNGNKSWGL V DLRDLREP ...String:
EEVNLENSQV ATREELKTSV GNVQTKLNIL RNENKEKIKN LRLELIQLME QGDQVVKSPW SSWQFGMNYF YENWRSTYKG SGDKSEKYV FNGIYTRGNW KVRNAMDMAE NQRVGGRPLT PGNDSLNSWK NASNSSGGGV TIDKDTSIGS STNGNKSWGL V DLRDLREP TNEVEILAHI SPKEVTKQVI SLNITEPTVQ TLEAPDVNPQ VNEPLPAPVI ELPEVETVTI NPLSINAPSA PT APSAPTI NIAITAPSAP VPPTINVVPA SPSTPSAPTI NIGIQPPSIT PLSITTPDSV DAPNVVSPQI KPVDFTVDPG GDS NVYSSE KHNSHQGWKA TWDKTINVTE LTNRNYVSLT RDVVDSTIPD DQVINVTKPN NRAMVVDEVR KNGIKVDFKG TINL QRSQN VGIDLQGTHQ GSISTPLIAN IYNSGKIIGN AKYGSTANKE QIAFGFNNAD GSNNTTMTNM VNKGEITLNA PSSAG IQLK PEDPHDWQPG APNYWNAAPL QIGNKTPNKI KGRVLMKADN QKDINLNGSG SFGMVTVFNE GVPKRLFAPS YVANYE NLR SERTYDGERV LPGGEIGRSA LSDSKYTSGV YNTGNINING DSSIGVGLLQ EIQEVKLAGN INIGTKAVAQ ETDISNL PN AGSKTYDKNK VEEAVGVFAG VPTMPVKPGE KDTLINSSGA RNTATSLVGT ETVEINGNIS LGEHATQSIG ALVGDTEI D LNKGQLTENG VNKGSNVDRK LKRSGDITAK SNSVINVGGK KNYGFVVSNS AHSSKFGTTV DSLEYNVDKT HHGKGINEG IINIIGDESV GFAMIKGGNS KSSGTISVKD NAENSIGFYG KEDSFTNSGT IEVTSAKKKN KAVVLDGTNA SNKINFTNTG NIYVNTSDN NNTNLDGNGN IGIYAQGNYK VEHNSGIVKA GKDVIAFYVK DSTGEVNINA PIELANSSKG TTIGIYSDGN A KVKFGTGS KLKIGEKAVG LYSADPTKFN NTFKIESGKT LDVELGKNST FGLLNGNNTV TNSPLLSKYL NNNTSDKINI VS FGEGASL FYATSKAKAI LDEDYKVTNG DAISTAVLVA NNGANVEIAS GKKLETNTNA GLIAINGTVG FTSVAKNNGT LIS TRIDKG IGIYTSAANG ENSGTITMQN KNAVGILGSK DSNLKNTGKI ELEAVSSAGV YAEDSNMINS GTTSEIIVNK ETSV GIYAK ETSISSVSKN VKNEGKIEIK ADGDGKSAGI YSKKEGGAKL TIENTGNIEV AQKASAGIYA KNESTQANTQ SEVTN SGLV KMSAENSIGI MGEKSKITNT GTGTKGIEIV EKKSAGILVT NESAVINSGR ISLSNSSISA SSDGLVGISV DGSSTG END ASGEIKVDAA YSTGMLSSGG GITNAGKIAL EKKESVGMYA TNANVTNSGA TPKGIFIKDE KSVGIYSKIN SSSIANK TV TNSGTIDIAG TSKTGSAGIY SIIESGATKK LSVVNNGNIT INQKKSVGIY AKNESSHANT ESDVTNSGKI EVKNEGSA G VLAEKYKVTN TGSGTNGIIV SAKKSAGIIG KLGSEIINSG IIKTEIATPT VATDGVVGIS LNNSKATNTS GGVITLDTD YSTGMYGEAN SQLTNEGNIT GTNKEYIVGM AGDSSTVTNK NIITLNGKKA TGIFGKNSST LLNETTGKIT TKEEESVGMY SSSSLKATN KGTIITEKKT SAGMLGDKAN IENDSSITTK EEMSAGMYVK NGTSKATNKG TVTTEKKTSA GILAEIDEAN G GTVSGLNE TTGTITVSEE TSAGMLGKVK SAVTASTAKL SLTNKKDINI NTKNSAGIMV VNESTAVGKE NVLAENTGII NL TSSSATN EKNIGILANK ATGINTGNIN VNSKESIGML GQNASSITNN KTITLSGEKG IGMLSKDTSS IADNNDTINV NGK ESLGML GEDSGTVKNN KTISVTAEKG VGIFVRDNGV GKGSGTGENT STGTITLENK EAVGIFAKNN GTSDSAKNSG TINL GKADG STIKESLIGM FAQAEAGKKA NVKNTKDINV NTKKSVGIYA KNDASNITDV DLENTGDINI NSKESAGVYA PKANI SKVG TITLKNSIDS NGSSAVYVSK GGKVANTAGA KINLGTVNQN RVAYYVNGKD SALAGADIGK ITGYGVGVYL QGTSGD KAT LDKNTSKLDY TLQGTGNGII GLLLKGETDI QSYTKGIKVG NTVAATSPSD KAKYAIGIYA DAQGTAGTPY NITTPIT AG KSGVGIFADK DSNINYTGNM EIGDGTTAGT GIFITKKIGA TGGKVTLGTN TIKLKGTKGV VAIASEGTTF NGGNATIE L VGSNIQGVGV YAKKGSTVNI DHWTFNNNGN SAEEVRSEEG RVYINANKNL KPKMVLTHVI NGETSIATGK TVTSVNDGS ITAKENIGLM AEGIKNHSMT WQEGNFEAVN HGIIDFSAAE KSTAMFINSA RAKNDGTIKV GKNSIGIYGF YNKDTRKYDG ASTNPDPNK LELETTSNSK MSLGDASTGM YLTNAEKIEN KGGQITSESG ATKNVGIYAV NGQDTKVSAN NKILNMTTAT N INLGNGSV GLYSKGQSNT VRNTVTNTGD ITVGDKITGS PSVAMYAENT NLTTNSKITV GKDGIAFYGK NSDITAKGSA NF SNKGVLA YLENSKFVSH LGNLGSTQNT MLYLKNSIAQ LDGAGTKVDM DVADGYTGAY IEGNSTLTGV KTIKLGQDST GLF LKDANF VSNAESITGT KDKARGILAT NSNLTNNSKI FLSGAESIGI YSNANNTKSV VNNGELTIAG KKTLGVFLKG SQSF ENKAN INIADSANSL EPTIGIYTAE GSSNIKHTSG TIDVGQKSIG IYSTTNSNVE MNGGKIHVKD QGVGIYKQNG KATIK GELD IDTHIATTKD SEPTGVYAVN GTEINDQASK ISIGAKSYGF ILNNTDPNKT NIYTNTDAGT VSLGNDSVFL YSNGKA NII NNRTINANGA SHLIAFYIKN GGNFTNNGTI DFSTGKGNIG IYAPGGKATN KGRVYVGKTD DIDPMTGKVY SDVSKIV YG IGMAADNGGY IKNDGEIRIY NNKSIGMYGK GIGTTVENTG KIYLDGSRAT ATDKIQSMTG VYVDDGAKFI NRGEIRTT D SYAGRDGKVN ENVTGLVGVA VMNGSTLENH GKILIDADNS YGVIIRGKRD SKGNVERYAV IKNYGEIKVR GKGTWGISW KDVSQAYIDE LQKQINDKIS SDPEGQALRA GSAHHHHHHH HSAGENLYFQ

UniProtKB: Outer membrane autotransporter barrel domain protein

-
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, 200 mM NaCl, pH 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV

-
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

+
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: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 151825
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: FLEXIBLE FIT
Output model

PDB-9qe7:
Membrane-distal part of extracellular domain of the Fap2 autotransporter adhesin from Fusobacterium nucleatum ATCC23726

+
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