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- EMDB-47348: Cryo-EM structure of TatBC-CueO signal peptide complex from Nitra... -

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Basic information

Entry
Database: EMDB / ID: EMD-47348
TitleCryo-EM structure of TatBC-CueO signal peptide complex from Nitratifractor salsuginis
Map datadeepemhanced map used for model refinement
Sample
  • Complex: TatBC-CueO signal peptide complex
    • Protein or peptide: Multicopper oxidase CueO
    • Protein or peptide: Sec-independent protein translocase protein TatB homolog
    • Protein or peptide: Sec-independent protein translocase protein TatC
KeywordsMembrane Protein / TatC / TatB / twin-arginine translocation / CueO / TRANSLOCASE
Function / homology
Function and homology information


proton motive force dependent protein transmembrane transporter activity / TAT protein transport complex / protein transport by the Tat complex / intracellular protein transmembrane transport / protein transmembrane transporter activity / copper ion binding
Similarity search - Function
Sec-independent protein translocase protein TatB / Sec-independent periplasmic protein translocase, conserved site / TatC family signature. / Sec-independent protein translocase protein TatA/B/E / mttA/Hcf106 family / Sec-independent periplasmic protein translocase TatC / Sec-independent protein translocase protein (TatC) / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase ...Sec-independent protein translocase protein TatB / Sec-independent periplasmic protein translocase, conserved site / TatC family signature. / Sec-independent protein translocase protein TatA/B/E / mttA/Hcf106 family / Sec-independent periplasmic protein translocase TatC / Sec-independent protein translocase protein (TatC) / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin
Similarity search - Domain/homology
Multicopper oxidase CueO / Sec-independent protein translocase protein TatC / Sec-independent protein translocase protein TatB homolog
Similarity search - Component
Biological speciesNitratifractor salsuginis (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDeme JC / Bryant OJ / Berks BC / Lea SM
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L000776/1 United Kingdom
Wellcome Trust107929/Z/15/Z United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To Be Published
Title: Structure of the twin-arginine protein translocation pathway core complex and the molecular basis for substrate recognition
Authors: Deme JC / Bryant OJ / Berks BC / Lea SM
History
DepositionOct 17, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47348.png

Downloads & links

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Map

FileDownload / File: emd_47348.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdeepemhanced map used for model refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.034051068 - 1.6207622
Average (Standard dev.)0.0008994465 (±0.019157631)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47348_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_47348_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: mask used for FSC calculation

Fileemd_47348_additional_2.map
Annotationmask used for FSC calculation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_47348_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_47348_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TatBC-CueO signal peptide complex

EntireName: TatBC-CueO signal peptide complex
Components
  • Complex: TatBC-CueO signal peptide complex
    • Protein or peptide: Multicopper oxidase CueO
    • Protein or peptide: Sec-independent protein translocase protein TatB homolog
    • Protein or peptide: Sec-independent protein translocase protein TatC

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Supramolecule #1: TatBC-CueO signal peptide complex

SupramoleculeName: TatBC-CueO signal peptide complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nitratifractor salsuginis (bacteria)

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Macromolecule #1: Multicopper oxidase CueO

MacromoleculeName: Multicopper oxidase CueO / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 3.157733 KDa
SequenceString:
MQRRDFLKYS VALGVASALP LWSRAVFA

UniProtKB: Multicopper oxidase CueO

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Macromolecule #2: Sec-independent protein translocase protein TatB homolog

MacromoleculeName: Sec-independent protein translocase protein TatB homolog
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Nitratifractor salsuginis (bacteria)
Molecular weightTheoretical: 21.44168 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFGMGFSEIL VIALVAILFL GPDKLPEAMV QIAKFFNSVR KTINEAKSTF EEELHLKELK EEALSYRQSL SEVGSDISGF KNAISNHTD ELQEAIEIAR SGMPTDRLNE SVDDLLEEDE PTGETSQRPG VTEYKEMARK ALEEAENSAE AQTAETPSVE D KGPESSPK ...String:
MFGMGFSEIL VIALVAILFL GPDKLPEAMV QIAKFFNSVR KTINEAKSTF EEELHLKELK EEALSYRQSL SEVGSDISGF KNAISNHTD ELQEAIEIAR SGMPTDRLNE SVDDLLEEDE PTGETSQRPG VTEYKEMARK ALEEAENSAE AQTAETPSVE D KGPESSPK ESSRPAGFKH LDNEANAWSH PQFEK

UniProtKB: Sec-independent protein translocase protein TatB homolog

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Macromolecule #3: Sec-independent protein translocase protein TatC

MacromoleculeName: Sec-independent protein translocase protein TatC / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Nitratifractor salsuginis (bacteria)
Molecular weightTheoretical: 42.954797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFESMKPHLA ELRQRLAISV LAVFVGFIIA FTFHNAILGW ITKPLNNALI QVGKIVEKRE MGTWKISGNE HNATLAPSKS PALLSDHAQ SAEKLHRTLA EASQATQNPK LQKLLSQAAS AAEELARNSR ILRKALVKEE NLTRQAVNQN LREKSFNGMI T THQVGGAF ...String:
MFESMKPHLA ELRQRLAISV LAVFVGFIIA FTFHNAILGW ITKPLNNALI QVGKIVEKRE MGTWKISGNE HNATLAPSKS PALLSDHAQ SAEKLHRTLA EASQATQNPK LQKLLSQAAS AAEELARNSR ILRKALVKEE NLTRQAVNQN LREKSFNGMI T THQVGGAF FVALKVSFFA GILMAMPVIL WQLWLFIAPG LYDNEKKMVL PFVVGGSVMF LIGVLFAYYV VTPFGFQFLI TF GSFLYTP LINIEDYVGF FTKILIGFGI AFELPVVAYF LALLGLITDK TLKDYFKYAI VIIFLLAAFL TPPDVLTQLL MAA PLILLY GLSILIVHYV NPYKPEEKED DEEEEEDEFE KAEREFEALE KGSESHESGS ENLYFQ

UniProtKB: Sec-independent protein translocase protein TatC

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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 BIOQUANTUM (6k x 4k) / Average electron dose: 56.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84834
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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