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- PDB-9xzn: Teichoic acid flippase TacF from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 9xzn
TitleTeichoic acid flippase TacF from Streptococcus pneumoniae
ComponentsSoluble cytochrome b562,Teichoic acid subunit flippase
KeywordsMEMBRANE PROTEIN / Teichoic acid / Flippase / Transporter / Lipid transport
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding / plasma membrane
Similarity search - Function
Polysaccharide biosynthesis protein / : / Polysaccharide biosynthesis protein / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Soluble cytochrome b562 / Teichoic acid subunit flippase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptococcus pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsCebrero, G. / Chidananda, H.A. / Denereaz, J.L. / Cester, E. / Mathew, A.T. / Bhowmik, D.R. / Capitani, M. / Reymond, J.L. / Kannan, N. / Veening, J.W. ...Cebrero, G. / Chidananda, H.A. / Denereaz, J.L. / Cester, E. / Mathew, A.T. / Bhowmik, D.R. / Capitani, M. / Reymond, J.L. / Kannan, N. / Veening, J.W. / Mehdipour, A.R. / Perez, C.
Funding support Switzerland, United States, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_207974 Switzerland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM158187 United States
CitationJournal: bioRxiv / Year: 2026
Title: Mechanistic basis of teichoic acid transport by a gatekeeper flippase.
Authors: Gonzalo Cebrero / Amrutha H Chidananda / Eric Cester / Julien Dénéréaz / Elif Sena Demir / Alen T Mathew / D Ryan Bhowmik / Mario de Capitani / Jean-Louis Reymond / Natarajan Kannan / ...Authors: Gonzalo Cebrero / Amrutha H Chidananda / Eric Cester / Julien Dénéréaz / Elif Sena Demir / Alen T Mathew / D Ryan Bhowmik / Mario de Capitani / Jean-Louis Reymond / Natarajan Kannan / Fikri Y Avci / Jan-Willem Veening / Ahmad Reza Mehdipour / Camilo Perez
Abstract: The cell wall is a complex structure that protects bacteria from environmental threats. Phosphocholine-containing teichoic acids are key cell wall biopolymers critical for host colonization, immune ...The cell wall is a complex structure that protects bacteria from environmental threats. Phosphocholine-containing teichoic acids are key cell wall biopolymers critical for host colonization, immune evasion, competence, and persistence in . The flippase TacF, a member of the multidrug/oligosaccharide-lipid/polysaccharide (MOP) superfamily, monitors the phosphocholine content of teichoic acids during transport, yet the underlying mechanism of this process remains unknown. We present a cryo-EM structure of TacF in lipid nanodiscs. complementation assays and molecular dynamics simulations reveal key residues involved in teichoic acid recognition and transport, while coevolutionary and conservation analyses delineate common mechanistic elements among MOP flippases, indicating a shared mechanism for polyprenyl-diphosphate-linked oligosaccharide lipid transport. Our findings provide mechanistic insights into an essential flippase involved in pathogenesis and a potential drug target.
History
DepositionAug 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 20, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1May 20, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Soluble cytochrome b562,Teichoic acid subunit flippase


Theoretical massNumber of molelcules
Total (without water)67,5751
Polymers67,5751
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 Soluble cytochrome b562,Teichoic acid subunit flippase / Cytochrome b-562


Mass: 67575.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: cybC, spr1150 / Strain: R6 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7, UniProt: Q8DPI1
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

Component
IDNameTypeEntity IDParent-IDSource
1BRIL-TacF with bound FabCOMPLEXall0MULTIPLE SOURCES
2BRIL-TacFCOMPLEXall1RECOMBINANT
3BAG2 FabCOMPLEX1RECOMBINANT
Molecular weightValue: 0.0675 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Escherichia coli (E. coli)562
32Streptococcus pneumoniae (bacteria)171101R6
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.7.1particle selection
2PHENIX1.21.2_5419model refinement
3SerialEMimage acquisition
13cryoSPARCv4.7.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87891 / Symmetry type: POINT
RefinementHighest resolution: 3.63 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024777
ELECTRON MICROSCOPYf_angle_d0.4926493
ELECTRON MICROSCOPYf_dihedral_angle_d5.654647
ELECTRON MICROSCOPYf_chiral_restr0.037773
ELECTRON MICROSCOPYf_plane_restr0.003792

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