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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., Suppl.: Diskette Appendix To V. , No. , [Month], Filename:
Year: 2026
Title: Structure and conformational dynamics of the Pseudomonas CbrA transceptor
Authors: Orlando, M.A. / Shah, T. / Faber, M.W. / Bose, S. / Orlando, B.J.
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

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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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