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- EMDB-63882: The structure of the BfpBG complex in the T4bP system -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63882
TitleThe structure of the BfpBG complex in the T4bP system
Map data
Sample
  • Complex: The structure of the BfpBG complex in the T4bP system
    • Protein or peptide: Outer membrane lipoprotein BfpB
    • Protein or peptide: Lipoprotein
KeywordsSECRETIN FAMILY / C17 SYMMETRY / T4bP / PROTEIN TRANSPORT
Function / homology
Function and homology information


pilus assembly / protein secretion / cell outer membrane
Similarity search - Function
Secretin, N-terminal / Secretin N-terminal domain / Toxin co-regulated pilus biosynthesis protein Q, C-terminal / Toxin co-regulated pilus biosynthesis protein Q / : / Type II/III secretion system / Bacterial type II and III secretion system protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Lipoprotein / Outer membrane lipoprotein BfpB
Similarity search - Component
Biological speciesEscherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria) / Escherichia coli O127:H6 str. E2348/69 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsPei CC / Sun H / Yin M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The structure of the BfpBG complex in the T4bP system
Authors: Pei CC / Sun H / Yin M
History
DepositionMar 21, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63882.png

Downloads & links

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Map

FileDownload / File: emd_63882.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 450 pix.
= 396. Å		0.88 Å/pix.
x 450 pix.
= 396. Å		0.88 Å/pix.
x 450 pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-2.9182935 - 4.566716
Average (Standard dev.)0.0023548496 (±0.1537979)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63882_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63882_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 : The structure of the BfpBG complex in the T4bP system

EntireName: The structure of the BfpBG complex in the T4bP system
Components
  • Complex: The structure of the BfpBG complex in the T4bP system
    • Protein or peptide: Outer membrane lipoprotein BfpB
    • Protein or peptide: Lipoprotein

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Supramolecule #1: The structure of the BfpBG complex in the T4bP system

SupramoleculeName: The structure of the BfpBG complex in the T4bP system / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)

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Macromolecule #1: Outer membrane lipoprotein BfpB

MacromoleculeName: Outer membrane lipoprotein BfpB / type: protein_or_peptide / ID: 1 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O127:H6 str. E2348/69 (bacteria)
Molecular weightTheoretical: 56.512406 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: CSGNGFYKDN LGVIDKNILH ADTSLLKSKN KEHYKSSDMV SKTDSIYIGN SSFQTYHGEP LPGKLEGVHG IILRSSTPLG FDEVLSMIQ DSSGIPIVKH TTKDVISGGV SSKSLAATVA EKMNSATGGK STDQFDHLLL EVSSEHQLMD VNYQGALSTF L DKVAANYN ...String:
CSGNGFYKDN LGVIDKNILH ADTSLLKSKN KEHYKSSDMV SKTDSIYIGN SSFQTYHGEP LPGKLEGVHG IILRSSTPLG FDEVLSMIQ DSSGIPIVKH TTKDVISGGV SSKSLAATVA EKMNSATGGK STDQFDHLLL EVSSEHQLMD VNYQGALSTF L DKVAANYN LYWTYESGRI AFSNEETKRF SISILPGGKY TSKNSISSDS NSSSGSSGSS GSSSSDSGAE LKFDSDVDFW KD IENSIKL ILGSDGSYSI STSTSSVIVR TSSANMKKIN EYINTLNAQL ERQVTIDVAI YNVTTTDSSD LAMSLEALLK HNG GVLGSV STSNFAATSG TPSFTGYLNG NGDSSNQVLL NLLAEKGKVS VVTSASVTTM SGQPVPLKVG NDRTYVSEIG TVLS QSSTS TTASTSTVTS GFLMNLLPQV ADDGNILLQY GVTLSELVGS NNGFDQATVN GTVIQLPNVD STTFVQSSML RNGNT LVLA GYEKKRNESV DQGVGTTSFK LLGGALNGSA SRTVTVICIT PRIIDLKASG E

UniProtKB: Outer membrane lipoprotein BfpB

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Macromolecule #2: Lipoprotein

MacromoleculeName: Lipoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O127:H6 str. E2348/69 (bacteria)
Molecular weightTheoretical: 12.65615 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ESANKNEKLF SGDTTSVALQ ASERTIKNAK ADWSVIKGQT LYGVLSDWAQ QSGWTVLWHA NYNYTLNASA VFKDMSLDDA VKKLLESMG NVSPRVFIKF YNGNHVILVT QSPEG

UniProtKB: Lipoprotein

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.7 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 75445
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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