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- EMDB-75104: CbrXA SLC5-STAC domains -

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Basic information

Entry
Database: EMDB / ID: EMD-75104
TitleCbrXA SLC5-STAC domains
Map datamain map for CbrXA SLC5-STAC domains sharpened with -48 A^2 b-factor
Sample
  • Complex: CbrXA
    • Protein or peptide: MFS transporter
    • Protein or peptide: histidine kinase
  • Ligand: HEXADECANE
  • Ligand: HISTIDINE
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: water
KeywordsSLC / transporter / STAC / CbrA / TRANSPORT PROTEIN
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
Uncharacterized protein / histidine kinase
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.95 Å
AuthorsOrlando MA / Shah T / Faber MM / Chouhan V / Bose S / Orlando BJ
Funding support United States, 1 items
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 MA / Shah T / Faber MW / Bose S / Orlando BJ
History
DepositionJan 15, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75104.png

Downloads & links

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Map

FileDownload / File: emd_75104.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map for CbrXA SLC5-STAC domains sharpened with -48 A^2 b-factor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 320 pix.
= 233.92 Å		0.73 Å/pix.
x 320 pix.
= 233.92 Å		0.73 Å/pix.
x 320 pix.
= 233.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.3789476 - 0.70958006
Average (Standard dev.)0.00026344697 (±0.013865779)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 233.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened main map for CbrXA SLC5-STAC domains

Fileemd_75104_additional_1.map
Annotationunsharpened main map for CbrXA SLC5-STAC domains
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: main map for CbrXA SLC5-STAC domains sharpened with...

Fileemd_75104_additional_2.map
Annotationmain map for CbrXA SLC5-STAC domains sharpened with deepEMhancer and a "highRes" model
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_75104_half_map_1.map
Annotationhalf_map_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_75104_half_map_2.map
Annotationhalf_map_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CbrXA

EntireName: CbrXA
Components
  • Complex: CbrXA
    • Protein or peptide: MFS transporter
    • Protein or peptide: histidine kinase
  • Ligand: HEXADECANE
  • Ligand: HISTIDINE
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: water

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Supramolecule #1: CbrXA

SupramoleculeName: CbrXA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: 1:1 assembly of co-purified CbrX peptide with CbrA SLC5-STAC domains
Source (natural)Organism: Pseudomonas putida KT2440 (bacteria)
Molecular weightTheoretical: 74 KDa

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Macromolecule #1: MFS transporter

MacromoleculeName: MFS transporter / type: protein_or_peptide / ID: 1 / Details: CbrX peptide encoded upstream of CbrA / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas putida KT2440 (bacteria)
Molecular weightTheoretical: 6.99433 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MYIYRLVLLL VVGIYLFSPA IMDWWIEPTG AWYRPYLLWL ILIVVTFILQ SQRDADEL

UniProtKB: Uncharacterized protein

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Macromolecule #2: histidine kinase

MacromoleculeName: histidine kinase / type: protein_or_peptide / ID: 2 / Details: CbrA SLC5-STAC domains / Number of copies: 1 / Enantiomer: LEVO / EC number: histidine kinase
Source (natural)Organism: Pseudomonas putida KT2440 (bacteria)
Molecular weightTheoretical: 66.668109 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPMSFSLTQM ILISAGYLMV LFGVAWISER GLIPRSIIRH PLTYTLSLGV YASAWAFYGS VGLAYQYGYG FLACYLGVSG AFLLAPVLL YPILKITRTY QLSSLADLLA FRFRSTWAGA LTTIIMLIGV LPLLALQIQA VADSISILTG EPVKARVAFA F CTLIILFT ...String:
MPMSFSLTQM ILISAGYLMV LFGVAWISER GLIPRSIIRH PLTYTLSLGV YASAWAFYGS VGLAYQYGYG FLACYLGVSG AFLLAPVLL YPILKITRTY QLSSLADLLA FRFRSTWAGA LTTIIMLIGV LPLLALQIQA VADSISILTG EPVKARVAFA F CTLIILFT IFFGSRHIAT REKHEGLVFA IAFESVIKLL ALGGIGLYAL YGVFGGPHEL EVWLLQNQTA LAALHTPLQE GP WRTLLLV FFASAIVMPH MYHMAFTENL NPRSLVSASW GLPLFLLLMS LAVPLVLWAG LRLGASTNPE YFTLGLGIAA NNQ ALALLA YIGGLSAASG LIIVTTLALS GMALNHLVLP LYQPPAEGNI YRWLKWTRRA LIVAIITAGF MFYLSQNYHQ SLAN LGIVA FVATLQFLPG VLSVLYWPTA NRRGFIAGLL AGTLVWMVTM LLPLLGNLQG FYIPLLDMIY VLDDTSWHMA AIASL AANV LLFTLISLFT NASTEEVSAA EACAVDNVRR PQRRELHAAS PQEFATQLAK PLGAKAAQKE VEQALRDLYL PFDERR PYA LRRLRDRIEA NLSGLMGPSV AQDMVETFLP YKSGNHHHHH HHH

UniProtKB: histidine kinase

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Macromolecule #3: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 3 / Number of copies: 15 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Macromolecule #4: HISTIDINE

MacromoleculeName: HISTIDINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: HIS
Molecular weightTheoretical: 156.162 Da
Chemical component information

ChemComp-HIS:
HISTIDINE

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Macromolecule #5: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 5 / Number of copies: 2 / Formula: LMN
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 67 / 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

Concentration6 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMHEPES
150.0 mMpotassium chlorideKCl
5.0 mMbeta-mercaptoethanol
0.005 %lauryl maltose neopentyl glycol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: Pelco easyGlow. 45 mA for 45 seconds
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 17620 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6783853
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 376477
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

1-v6

chain_id: A, source_name: AlphaFold, initial_model_type: in silico modelcbrA

1-v6

chain_id: X, source_name: AlphaFold, initial_model_type: in silico modelcbrX
RefinementSpace: REAL
Output model

PDB-10ed:
CbrXA SLC5-STAC domains

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