[English] 日本語
Yorodumi
- EMDB-61458: Structure of cargo complex (BtpeA-BtaeB-BtapC) bound to the VgrG ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61458
TitleStructure of cargo complex (BtpeA-BtaeB-BtapC) bound to the VgrG spike from the Type VI secretion system
Map data
Sample
  • Complex: VgrG-BtpeA-BtaeB-BtapC quaternary complex
    • Protein or peptide: DUF3289 family protein
    • Protein or peptide: Peptidase C39-like domain-containing protein
    • Protein or peptide: Bacteroides T6SS Adapter Protein C
    • Protein or peptide: Type VI secretion system spike protein VgrG
  • Ligand: ZINC ION
KeywordsT6SS / Co-delivery / effector complex / VgrG spike / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


Conserved hypothetical protein CHP03034 / Protein of unknown function DUF4280 / Protein of unknown function (DUF3289) / Domain of unknown function (DUF4280) / Phage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily
Similarity search - Domain/homology
: / Phage baseplate assembly protein V / Uncharacterized protein / DUF3289 family protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsZheng SN / Li WX / Chen Z / Gao X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)323B2003 China
CitationJournal: Cell Host Microbe / Year: 2025
Title: A conserved adaptor orchestrates co-secretion of synergistic type VI effectors in gut Bacteroidota.
Authors: Weixun Li / Shuaining Zheng / Xiaoning Xu / Jing He / Xuyao Jiao / Mingyu Wang / Wei Hu / Shengying Li / Xianzhi Jiang / Bentley Lim / Feng Shao / Xiang Gao /
Abstract: Interbacterial competition is crucial for shaping microbial communities and is often mediated by type VI secretion systems (T6SSs) that inject effectors into competing bacteria. T6SS effectors are ...Interbacterial competition is crucial for shaping microbial communities and is often mediated by type VI secretion systems (T6SSs) that inject effectors into competing bacteria. T6SS effectors are released via structural proteins such as VgrG, but the secretion timing and coordination are unclear. Here, we report two effectors, BtpeA (Bacteroides T6SS phosphatase effector A) and BtaeB (Bacteroides T6SS amidase effector B), within the Bacteroidota T6SS that exert distinct cell-wall destructive activities critical for interspecies competition but whose secretion is interdependent. BtpeA and BtaeB co-secretion requires an adaptor protein, BtapC (Bacteroides T6SS adaptor protein C), that mediates the sequential assembly of the pre-firing complex, VgrG-BtpeA-BtaeB-BtapC. Structural analyses of this quaternary complex elucidate multi-cargo loading mechanisms with a conserved loop in BtaeB serving as a "checkpoint" to ensure BtpeA co-secretion. During mouse colonization, the combined activities of BtpeA and BtaeB significantly exceed the sum of the individual effectors. These findings unveil a T6SS-mediated co-delivery mechanism that ensures functional synergism of effectors, highlighting potential applications in modulating gut microbiota.
History
DepositionSep 6, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61458.png

Downloads & links

-
Map

FileDownload / File: emd_61458.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 480 pix.
= 566.4 Å		1.18 Å/pix.
x 480 pix.
= 566.4 Å		1.18 Å/pix.
x 480 pix.
= 566.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-7.2003336 - 10.759717999999999
Average (Standard dev.)-0.00092518405 (±0.15855825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 566.39996 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_61458_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61458_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : VgrG-BtpeA-BtaeB-BtapC quaternary complex

EntireName: VgrG-BtpeA-BtaeB-BtapC quaternary complex
Components
  • Complex: VgrG-BtpeA-BtaeB-BtapC quaternary complex
    • Protein or peptide: DUF3289 family protein
    • Protein or peptide: Peptidase C39-like domain-containing protein
    • Protein or peptide: Bacteroides T6SS Adapter Protein C
    • Protein or peptide: Type VI secretion system spike protein VgrG
  • Ligand: ZINC ION

-
Supramolecule #1: VgrG-BtpeA-BtaeB-BtapC quaternary complex

SupramoleculeName: VgrG-BtpeA-BtaeB-BtapC quaternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Bacteroides fragilis (bacteria)

-
Macromolecule #1: DUF3289 family protein

MacromoleculeName: DUF3289 family protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 68.774492 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGKEFVVDK AMCMCKYGAA PGKLMVTDNQ FFRLNGTKLC ASTMTLGNVI YPPGFGICKV NPMFPKPCVP AITQWNGQFS KITMMGGNP LTDKSKGTCS CGGPDCIEFM QTGQIPVPGS KQMQQATGEH QGELDAMGDP SALTKHPVDT PTSLLLKEGN I LVKAVKGE ...String:
MAGKEFVVDK AMCMCKYGAA PGKLMVTDNQ FFRLNGTKLC ASTMTLGNVI YPPGFGICKV NPMFPKPCVP AITQWNGQFS KITMMGGNP LTDKSKGTCS CGGPDCIEFM QTGQIPVPGS KQMQQATGEH QGELDAMGDP SALTKHPVDT PTSLLLKEGN I LVKAVKGE AESFSGQTLI YEVEHYNTPI VSDEIRSHVK WKVTIGEKEE TVDQPGTDVL ELSVKEEWQG KKLCVQAYIN QP SDNVKVN TQIKKWEFPI IVDRYKMPGL NDTGTDIADD MAYGYGVNTK KCVYSTLLIK QLIESYEQKH ENKKIDNILS NSI DYDPEP PMFSTSSLDT KQKMERYIRV KNAKAIYSKE DFPKISSRIQ EGVRFLRKGG DDFTDEELFA DFEAMAKLAF SSLN SEMRG NIVRMIAKFR QNNGGVYEDS VLTDHIKKHP STIRYCNQLE TYIKKELQDS KGDVSTLEDI KIFFKGERDL LEDIL KKRV NDKYHKKDFS LTPVYDAGFI SFKNIGRKTE QIKNATQGYT IALNDIWSTE VIIKKYVLNG NSYTVDYRVT LWDHFG LDA PDLEANKVAA YGAGFRAWFI LQHFRGYKPF ITKITFDKTF KGKIQ

UniProtKB: DUF3289 family protein

-
Macromolecule #2: Peptidase C39-like domain-containing protein

MacromoleculeName: Peptidase C39-like domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 69.103289 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDDKSQLTI SIDIKAEDRK YQIVENSVTS ILFKVSDTTT RYVYNIRMGE MRNESETTPE GLKNLNLKKE CDLSVKIRTE ADQAFVLSE KHRGNIMLVE FFKYEGIPVL CASCVLIVKP SDLKITQVIF KDSTGKEVGC GSVQYEANLK FALRVKYNRP L LRGEKAPK ...String:
MSDDKSQLTI SIDIKAEDRK YQIVENSVTS ILFKVSDTTT RYVYNIRMGE MRNESETTPE GLKNLNLKKE CDLSVKIRTE ADQAFVLSE KHRGNIMLVE FFKYEGIPVL CASCVLIVKP SDLKITQVIF KDSTGKEVGC GSVQYEANLK FALRVKYNRP L LRGEKAPK LKCKGYCTNA VTGEYEEISK FRVDENGAYT DTFYCDDGLQ ESHAGADYVF SFGINNPYGP PFMIEDTNVP VP SIQKIHL IGRNLKKPQI TSVIWSSKEM IKFGEDSPRR KSINYNEDGF LHIHARGMYG QKVRVELFEK DSTGIKKLLL GLK DDVTIL DNVVCVPVEM SGVYAKAAKG RHALAEGLSF EILAKVTPLD TSIAAFEQDD KSLIELQIYG KADEDKAAKS TVNG TMKFM IADVEEDEKG EEEKAIEEGV CPLCGKKHID LRSKIDYQTQ FDSRFGTKKE QNVACYKACK VILTNAGLSP NSAPN DNTV IQIGVEKSST DNSSHSSSLT IDFVKASEGL NYINQQLETG YPILVGVDYK AGSPNSDKTT DHFIVIVGRG CKNNEV YYL FYEVGTGQQE NGQYKGAHEN NKLYLKKDNT LQGTPYHNSN KKYIVVQIRK NILS

UniProtKB: UNIPROTKB: A0A5C6HES3

-
Macromolecule #3: Bacteroides T6SS Adapter Protein C

MacromoleculeName: Bacteroides T6SS Adapter Protein C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 29.83785 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYKFRNLKGQ YSINVSTTFP GSQASLYSAI IEVIASYQNV DDYFIFELRS RQEVKLNGNP PSQMVDLFML RLSNTYYPMK LKVSTSGKI MEVINFTDIK ERWEAECAKI VEEIPCIAYE QYIELSKSNM DTENVFLQAL RKDSFIQFYF KEYLDDIDIV C YNFPRRGE ...String:
MYKFRNLKGQ YSINVSTTFP GSQASLYSAI IEVIASYQNV DDYFIFELRS RQEVKLNGNP PSQMVDLFML RLSNTYYPMK LKVSTSGKI MEVINFTDIK ERWEAECAKI VEEIPCIAYE QYIELSKSNM DTENVFLQAL RKDSFIQFYF KEYLDDIDIV C YNFPRRGE STFYDLAIDS DGSFHKDIKT FHVKEYNSKR YSGKLICEYS EENDIFSLIA EFYYNTLDGQ CKKKVSISVE NR SVQKANK LKSFLFD

UniProtKB: Uncharacterized protein

-
Macromolecule #4: Type VI secretion system spike protein VgrG

MacromoleculeName: Type VI secretion system spike protein VgrG / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 68.113883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASTNLDAVS VEIKVAGKVC DYVTMELFQS VSTHHRFKIK VNYRPDKPSV WAIGPDVIFK QLGEKVSIIM THHESGEKTE FHGLISDIH VEGFDGNQGF VILEGGSPTI LLDRDPAMDC YVEQNLNTIV SDILDKSGVK MNVTNNPKHT DIIPYVARYK E TSYGFLSR ...String:
MASTNLDAVS VEIKVAGKVC DYVTMELFQS VSTHHRFKIK VNYRPDKPSV WAIGPDVIFK QLGEKVSIIM THHESGEKTE FHGLISDIH VEGFDGNQGF VILEGGSPTI LLDRDPAMDC YVEQNLNTIV SDILDKSGVK MNVTNNPKHT DIIPYVARYK E TSYGFLSR LLRSYGEWFY YNGETLQIGN PEIETESRAG YDVDLTGVSI NATIRSLNHS TYEFDPVNDK FYYDYSGTPK GA TLGSRSA EKCSEPIFPT EAKLPSMRPA YSAMDLEHYG DAGFHRNYSQ LSQIKASSRY CGIRLGELVV TRVPESFPGV KIT DLGRYR ITEITHTVDG QGRYSNTFCG VPGGTPVMPW GDAVMPVAYP EMARVVSNED PKNQGRVKVQ FMWQEVDGGE SYWM RVQSP DAGKSDQVAK NRGFVFIPEP GDLVMVGFEQ GNPDRPYVTG SLFYKANSQG AATDNTVKSI RTRSGHTLEF NDDEG GDWG ITIKDRNGCM FHFDTKGKNI EITAPETMTL NAQNININAG EQLNTSSGKE TVMQIGTDFQ QDVGGNAEIA IGESLT ESI AKDSTNSIAG NLSVTVDENL MYDAQDMTLT AQGGMKLLAN AKIGLKSSEG VDIAQ

UniProtKB: Phage baseplate assembly protein V

-
Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106021
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
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