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- EMDB-47345: Cryo-EM structure of a TatBC-MdoD complex from Escherichia coli -

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Basic information

Entry
Database: EMDB / ID: EMD-47345
TitleCryo-EM structure of a TatBC-MdoD complex from Escherichia coli
Map datadeepemhanced map used for model refinement
Sample
  • Complex: TatBC-MdoD complex
    • Protein or peptide: Sec-independent protein translocase protein TatB
    • Protein or peptide: Sec-independent protein translocase protein TatC
    • Protein or peptide: Glucans biosynthesis protein D
  • Ligand: water
KeywordsMembrane Protein / TatC / TatB / twin-arginine translocation / MdoD / signal peptide / 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 / beta-glucan biosynthetic process / intracellular protein transmembrane transport / catalytic activity / protein transmembrane transporter activity / outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
Glucan biosynthesis, MdoD / Glucan biosynthesis, periplasmic, MdoG C-terminal / Glucan biosynthesis protein MdoG/MdoD / Periplasmic glucan biosynthesis protein, MdoG / 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) / Glycoside hydrolase-type carbohydrate-binding ...Glucan biosynthesis, MdoD / Glucan biosynthesis, periplasmic, MdoG C-terminal / Glucan biosynthesis protein MdoG/MdoD / Periplasmic glucan biosynthesis protein, MdoG / 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) / Glycoside hydrolase-type carbohydrate-binding / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Galactose mutarotase-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Glucans biosynthesis protein D / 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: 2.4 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

Downloads & links

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Map

FileDownload / File: emd_47345.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdeepemhanced map used for model refinement
Voxel sizeX=Y=Z: 0.693 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.043040827 - 1.9653133
Average (Standard dev.)0.00018580903 (±0.012201672)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 354.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : TatBC-MdoD complex

EntireName: TatBC-MdoD complex
Components
  • Complex: TatBC-MdoD complex
    • Protein or peptide: Sec-independent protein translocase protein TatB
    • Protein or peptide: Sec-independent protein translocase protein TatC
    • Protein or peptide: Glucans biosynthesis protein D
  • Ligand: water

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Supramolecule #1: TatBC-MdoD complex

SupramoleculeName: TatBC-MdoD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Sec-independent protein translocase protein TatB

MacromoleculeName: Sec-independent protein translocase protein TatB / type: protein_or_peptide / ID: 1 / 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 #2: Sec-independent protein translocase protein TatC

MacromoleculeName: Sec-independent protein translocase protein TatC / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 29.969305 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 ERSHHHHHH

UniProtKB: Sec-independent protein translocase protein TatC

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Macromolecule #3: Glucans biosynthesis protein D

MacromoleculeName: Glucans biosynthesis protein D / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 62.916844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMDRRRFIKG SMAMAAVCGT SGIASLFSQA AFAADSDIAD GQTQRFDFSI LQSMAHDLAQ TAWRGAPRPL PDTLATMTPQ AYNSIQYDA EKSLWHNVEN RQLDAQFFHM GMGFRRRVRM FSVDPATHLA REIHFRPELF KYNDAGVDTK QLEGQSDLGF A GFRVFKAP ...String:
SMDRRRFIKG SMAMAAVCGT SGIASLFSQA AFAADSDIAD GQTQRFDFSI LQSMAHDLAQ TAWRGAPRPL PDTLATMTPQ AYNSIQYDA EKSLWHNVEN RQLDAQFFHM GMGFRRRVRM FSVDPATHLA REIHFRPELF KYNDAGVDTK QLEGQSDLGF A GFRVFKAP ELARRDVVSF LGASYFRAVD DTYQYGLSAR GLAIDTYTDS KEEFPDFTAF WFDTVKPGAT TFTVYALLDS AS ITGAYKF TIHCEKSQVI MDVENHLYAR KDIKQLGIAP MTSMFSCGTN ERRMCDTIHP QIHDSDRLSM WRGNGEWICR PLN NPQKLQ FNAYTDNNPK GFGLLQLDRD FSHYQDIMGW YNKRPSLWVE PRNKWGKGTI GLMEIPTTGE TLDNIVCFWQ PEKA VKAGD EFAFQYRLYW SAQPPVHCPL ARVMATRTGM GGFSEGWAPG EHYPEKWARR FAVDFVGGDL KAAAPKGIEP VITLS SGEA KQIEILYIEP IDGYRIQFDW YPTSDSTDPV DMRMYLRCQG DAISETWLYQ YFPPAPDKRQ YVDDRVMS

UniProtKB: Glucans biosynthesis protein D

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 52.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 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: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1201445
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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