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- EMDB-53848: Trimer TatBC complex with bound substrate SufI -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53848
TitleTrimer TatBC complex with bound substrate SufI
Map data
Sample
  • Complex: twin-arginine translocase
    • Protein or peptide: Sec-independent protein translocase protein TatC
    • Protein or peptide: Sec-independent protein translocase protein TatB
    • Protein or peptide: Cell division protein FtsP
Keywordsmembrane protein / twin-arginine translocase / 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 / FtsZ-dependent cytokinesis / cell division site / response to ionizing radiation / response to stress / transmembrane protein transporter activity / response to radiation ...proton motive force dependent protein transmembrane transporter activity / TAT protein transport complex / protein transport by the Tat complex / intracellular protein transmembrane transport / FtsZ-dependent cytokinesis / cell division site / response to ionizing radiation / response to stress / transmembrane protein transporter activity / response to radiation / outer membrane-bounded periplasmic space / response to oxidative stress / oxidoreductase activity / copper ion binding / cell division / protein homodimerization activity / membrane / identical protein binding / plasma membrane
Similarity search - Function
Cell division protein FtsP / Sec-independent protein translocase protein TatB / Sec-independent periplasmic protein translocase, conserved site / TatC family signature. / Sec-independent periplasmic protein translocase TatC / Sec-independent protein translocase protein (TatC) / Sec-independent protein translocase protein TatA/B/E / mttA/Hcf106 family / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Multicopper oxidase, C-terminal ...Cell division protein FtsP / Sec-independent protein translocase protein TatB / Sec-independent periplasmic protein translocase, conserved site / TatC family signature. / Sec-independent periplasmic protein translocase TatC / Sec-independent protein translocase protein (TatC) / Sec-independent protein translocase protein TatA/B/E / mttA/Hcf106 family / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Multicopper oxidase, C-terminal / 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
Cell division protein FtsP / Sec-independent protein translocase protein TatC / Sec-independent protein translocase protein TatB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhao Z / Sazanov L
Funding support Austria, 1 items
OrganizationGrant numberCountry
Other privatehttps://ist.ac.at/en/home Austria
CitationJournal: To Be Published
Title: Trimer TatBC complex with bound substrate SufI
Authors: Zhao Z / Sazanov L
History
DepositionMay 18, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53848.png

Downloads & links

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Map

FileDownload / File: emd_53848.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 460 pix.
= 487.6 Å		1.06 Å/pix.
x 460 pix.
= 487.6 Å		1.06 Å/pix.
x 460 pix.
= 487.6 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: 0.02
Minimum - Maximum-0.061955016 - 0.12577856
Average (Standard dev.)0.00013368312 (±0.0018164235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 487.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53848_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_53848_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 : twin-arginine translocase

EntireName: twin-arginine translocase
Components
  • Complex: twin-arginine translocase
    • Protein or peptide: Sec-independent protein translocase protein TatC
    • Protein or peptide: Sec-independent protein translocase protein TatB
    • Protein or peptide: Cell division protein FtsP

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Supramolecule #1: twin-arginine translocase

SupramoleculeName: twin-arginine translocase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Sec-independent protein translocase protein TatC

MacromoleculeName: Sec-independent protein translocase protein TatC / type: protein_or_peptide / ID: 1 / Details: flag tag / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 31.758975 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVEDTQPLI THLIELRKRL LNCIIAVIVI FLCLVYFAND IYHLVSAPLI KQLPQGSTMI ATDVASPFFT PIKLTFMVSL ILSAPVILY QVWAFIAPAL YKHERRLVVP LLVSSSLLFY IGMAFAYFVV FPLAFGFLAN TAPEGVQVST DIASYLSFVM A LFMAFGVS ...String:
MSVEDTQPLI THLIELRKRL LNCIIAVIVI FLCLVYFAND IYHLVSAPLI KQLPQGSTMI ATDVASPFFT PIKLTFMVSL ILSAPVILY QVWAFIAPAL YKHERRLVVP LLVSSSLLFY IGMAFAYFVV FPLAFGFLAN TAPEGVQVST DIASYLSFVM A LFMAFGVS FEVPVAIVLL CWMGITSPED LRKKRPYVLV GAFVVGMLLT PPDVFSQTLL AIPMYCLFEI GVFFSRFYVG KG RNREEEN DAEAESEKTE EGSDYKDHDG DYKDHDIDYK DDDDK

UniProtKB: Sec-independent protein translocase protein TatC

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Macromolecule #2: Sec-independent protein translocase protein TatB

MacromoleculeName: Sec-independent protein translocase protein TatB / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.441818 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MFDIGFSELL LVFIIGLVVL GPQRLPVAVK TVAGWIRALR SLATTVQNEL TQELKLQEFQ DSLKKVEKAS LTNLTPELKA SMDELRQAA ESMKRSYVAN DPEKASDEAH TIHNPVVKDN EAAHEGVTPA AAQTQASSPE QKPETTPEPV VKPAADAEPK T AAPSPSSS DKP

UniProtKB: Sec-independent protein translocase protein TatB

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Macromolecule #3: Cell division protein FtsP

MacromoleculeName: Cell division protein FtsP / type: protein_or_peptide / ID: 3 / Details: His8tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 53.00902 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLSRRQFIQ ASGIALCAGA VPLKASAAGQ QQPLPVPPLL ESRRGQPLFM TVQRAHWSFT PGTRASVWGI NGRYLGPTIR VWKGDDVKL IYSNRLTENV SMTVAGLQVP GPLMGGPARM MSPNADWAPV LPIRQNAATL WYHANTPNRT AQQVYNGLAG M WLVEDEVS ...String:
MSLSRRQFIQ ASGIALCAGA VPLKASAAGQ QQPLPVPPLL ESRRGQPLFM TVQRAHWSFT PGTRASVWGI NGRYLGPTIR VWKGDDVKL IYSNRLTENV SMTVAGLQVP GPLMGGPARM MSPNADWAPV LPIRQNAATL WYHANTPNRT AQQVYNGLAG M WLVEDEVS KSLPIPNHYG VDDFPVIIQD KRLDNFGTPE YNEPGSGGFV GDTLLVNGVQ SPYVEVSRGW VRLRLLNASN SR RYQLQMN DGRPLHVISG DQGFLPAPVS VKQLSLAPGE RREILVDMSN GDEVSITCGE AASIVDRIRG FFEPSSILVS TLV LTLRPT GLLPLVTDSL PMRLLPTEIM AGSPIRSRDI SLGDDPGING QLWDVNRIDV TAQQGTWERW TVRADEPQAF HIEG VMFQI RNVNGAMPFP EDRGWKDTVW VDGQVELLVY FGQPSWAHFP FYFNSQTLEM ADRGSIGQLL VNPVPHHHHH HHH

UniProtKB: Cell division protein FtsP

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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

Concentration0.25 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
50.0 mMTrisTris
90.0 mMNaClsodium chloride
60.0 mMKClpotassium chloride

Details: 50 mM Tris-HCl pH7.6, 90 mM NaCl, 60 mM KCl, 0.2% Digitonin, 0.002% pmsf, protease inhibitor
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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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: 10177 / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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

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Image processing

CTF correctionSoftware - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Alphafold3 prediction from the Alphafold server
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Coot, PHENIX (ver. dev_4933+SVN)) / Number images used: 163739
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 5 / Avg.num./class: 263490 / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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