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- PDB-9e06: Cryo-EM structure of a TatBC complex from Nitratifractor salsugin... -

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Basic information

Entry
Database: PDB / ID: 9000000
TitleCryo-EM structure of a TatBC complex from Nitratifractor salsuginis in nanodisc
Components
  • Sec-independent protein translocase protein TatB homolog
  • Sec-independent protein translocase protein TatC
KeywordsTRANSLOCASE / Membrane Protein / TatC / TatB / twin-arginine translocation
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
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)
Similarity search - Domain/homology
Sec-independent protein translocase protein TatC / Sec-independent protein translocase protein TatB homolog
Similarity search - Component
Biological speciesNitratifractor salsuginis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDeme, J.C. / Bryant, O.J. / Berks, B.C. / Lea, S.M.
Funding support United Kingdom, United States, 3items
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, J.C. / Bryant, O.J. / Berks, B.C. / Lea, S.M.
History
DepositionOct 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0Aug 27, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Aug 27, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Sec-independent protein translocase protein TatB homolog
A: Sec-independent protein translocase protein TatC
F: Sec-independent protein translocase protein TatB homolog
D: Sec-independent protein translocase protein TatB homolog
E: Sec-independent protein translocase protein TatC
C: Sec-independent protein translocase protein TatC


Theoretical massNumber of molelcules
Total (without water)193,1896
Polymers193,1896
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sec-independent protein translocase protein TatB homolog


Mass: 21441.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratifractor salsuginis (bacteria) / Gene: Nitsa_0635 / Production host: Escherichia coli (E. coli) / References: UniProt: E6X1H0
#2: Protein Sec-independent protein translocase protein TatC


Mass: 42954.797 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratifractor salsuginis (bacteria) / Gene: tatC, Nitsa_0634 / Production host: Escherichia coli (E. coli) / References: UniProt: E6X1G9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TatBC complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Nitratifractor salsuginis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 56.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 246675 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036840
ELECTRON MICROSCOPYf_angle_d0.4969291
ELECTRON MICROSCOPYf_dihedral_angle_d3.976878
ELECTRON MICROSCOPYf_chiral_restr0.0391113
ELECTRON MICROSCOPYf_plane_restr0.0041110

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