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- EMDB-61459: Structure of the BtpeA effector and BtaeB effector bound to the V... -

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Basic information

Entry
Database: EMDB / ID: EMD-61459
TitleStructure of the BtpeA effector and BtaeB effector bound to the VgrG spike from the Type VI secretion system
Map data
Sample
  • Complex: VgrG-BtpeA-BtaeB complex
    • Protein or peptide: DUF3289 family protein
    • Protein or peptide: Peptidase C39-like domain-containing protein
    • 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 / DUF3289 family protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 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: To Be Published
Title: Synergistic Function and Effector-Dependent Secretion in the Type VI Secretion System
Authors: Li WX / Zheng SN / Chen Z / Gao X
History
DepositionSep 6, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61459.png

Downloads & links

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Map

FileDownload / File: emd_61459.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: 0.8
Minimum - Maximum-5.131851 - 8.992292000000001
Average (Standard dev.)-0.0009323316 (±0.16884485)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #1

Fileemd_61459_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_61459_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 : VgrG-BtpeA-BtaeB complex

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

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Supramolecule #1: VgrG-BtpeA-BtaeB complex

SupramoleculeName: VgrG-BtpeA-BtaeB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Bacteroides fragilis (bacteria)

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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

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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

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Macromolecule #3: Type VI secretion system spike protein VgrG

MacromoleculeName: Type VI secretion system spike protein VgrG / type: protein_or_peptide / ID: 3 / 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

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
VitrificationCryogen name: ETHANE

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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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73616
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 112.3
Output model

PDB-9jg9:
Structure of the BtpeA effector and BtaeB effector bound to the VgrG spike from the Type VI secretion system

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