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- PDB-10ed: CbrXA SLC5-STAC domains -

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Basic information

Entry
Database: PDB / ID: 10ed
TitleCbrXA SLC5-STAC domains
Components
  • MFS transporter
  • histidine kinase
KeywordsTRANSPORT PROTEIN / SLC / transporter / STAC / CbrA
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / transmembrane transporter activity / regulation of DNA-templated transcription / ATP binding / membrane
Similarity search - Function
Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. ...Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / PAS fold / PAS fold / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
HISTIDINE / HEXADECANE / Uncharacterized protein / histidine kinase
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.95 Å
AuthorsOrlando, M.A. / Shah, T. / Faber, M.M. / Chouhan, V. / Bose, S. / Orlando, B.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM146721 United States
CitationJournal: Protein Sci / Year: 2026
Title: Structure and conformational dynamics of the Pseudomonas CbrA transceptor.
Authors: Melanie A Orlando / Tejas Shah / Matthew W Faber / Samik Bose / Benjamin J Orlando /
Abstract: The CbrA protein is a central regulator of carbon metabolism, biofilm formation, and virulence in Pseudomonas species, but the molecular mechanisms by which CbrA links nutrient sensing to downstream ...The CbrA protein is a central regulator of carbon metabolism, biofilm formation, and virulence in Pseudomonas species, but the molecular mechanisms by which CbrA links nutrient sensing to downstream signaling has remained unclear. CbrA is a rare "transceptor" that combines membrane transporter and histidine kinase domains into a single functional polypeptide. The structural basis for histidine recognition and membrane transport, as well as signaling through intracellular histidine kinase domains has remained elusive. Here we determined a cryo-EM structure of CbrA which provides key molecular details of the SLC5-STAC domains in this unusual system. Unexpectedly, the small peptide CbrX encoded upstream of CbrA formed a stable complex with the SLC5 transporter domain, but was not essential for growth of Pseudomonas putida on histidine as a sole carbon source. The cryo-EM structure reveals how histidine binds within the transporter, and molecular dynamics simulations provide insight into proton gradient driven conformational changes that enable histidine transport. These findings define the molecular architecture of key CbrA functional domains, and lay the foundation for developing a comprehensive understanding of coupling between membrane transport and downstream signaling pathways that guide essential physiological traits in Pseudomonas.
History
DepositionJan 15, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Sep 2, 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
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: MFS transporter
A: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,22620
Polymers73,6622
Non-polymers5,56318
Water1,20767
1


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

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Components

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Protein , 2 types, 2 molecules XA

#1: Protein MFS transporter


Mass: 6994.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CbrX peptide encoded upstream of CbrA / Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: PP_5704 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A140FWQ6
#2: Protein histidine kinase


Mass: 66668.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CbrA SLC5-STAC domains / Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: PP_4695 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q88DX3, histidine kinase

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Non-polymers , 4 types, 85 molecules

#3: Chemical
ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C16H34
#4: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: CbrXA / Type: COMPLEX
Details: 1:1 assembly of co-purified CbrX peptide with CbrA SLC5-STAC domains
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.074 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas putida KT2440 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C41(DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPES1
2150 mMpotassium chlorideKCl1
35 mMbeta-mercaptoethanol1
40.005 %lauryl maltose neopentyl glycol1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Pelco easyGlow. 45 mA for 45 seconds / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 165000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17620
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
4cryoSPARC4.7.1CTF correction
7UCSF Chimera1.17.3model fitting
9cryoSPARC4.7.1initial Euler assignment
10cryoSPARC4.7.1final Euler assignment
12cryoSPARC4.7.13D reconstruction
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6783853
3D reconstructionResolution: 1.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 376477 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building

3D fitting-ID: 1 / Source name: AlphaFold / Type: in silico model

IDAccession codeChain-IDDetails (eV)Initial refinement model-ID
1AF-Q88DX3-F1-v6AcbrA1
2AF-A0A140FWQ6-F1-v6XcbrX2
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035508
ELECTRON MICROSCOPYf_angle_d0.5577446
ELECTRON MICROSCOPYf_dihedral_angle_d11.5911033
ELECTRON MICROSCOPYf_chiral_restr0.038868
ELECTRON MICROSCOPYf_plane_restr0.004875

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