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- PDB-9kjc: Cryo-EM structure of BL-bound atABCB19 in lipid nanodisc -

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Basic information

Entry
Database: PDB / ID: 9kjc
TitleCryo-EM structure of BL-bound atABCB19 in lipid nanodisc
ComponentsABC transporter B family member 19
KeywordsMEMBRANE PROTEIN / ABCB19 / Plant hormone transport / BL-bound
Function / homology
Function and homology information


acropetal auxin transport / formation of plant organ boundary / basipetal auxin transport / auxin transport / anthocyanin accumulation in tissues in response to UV light / response to red or far red light / lateral root development / stamen development / positive gravitropism / response to far red light ...acropetal auxin transport / formation of plant organ boundary / basipetal auxin transport / auxin transport / anthocyanin accumulation in tissues in response to UV light / response to red or far red light / lateral root development / stamen development / positive gravitropism / response to far red light / auxin efflux transmembrane transporter activity / auxin polar transport / root development / response to blue light / photomorphogenesis / response to auxin / auxin-activated signaling pathway / regulation of cell size / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Brassinolide / ABC transporter B family member 19
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu, Y. / Liao, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of BL-bound atABCB19 in lipid nanodisc
Authors: Liu, Y.
History
DepositionNov 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: ABC transporter B family member 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,4132
Polymers136,9331
Non-polymers4811
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 ABC transporter B family member 19 / ABC transporter ABCB.19 / AtABCB19 / Multidrug resistance protein 11 / P-glycoprotein 19


Mass: 136932.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABCB19, MDR1, MDR11, PGP19, At3g28860, MLD15.2 / Production host: Homo sapiens (human) / References: UniProt: Q9LJX0
#2: Chemical ChemComp-BLD / Brassinolide / (3aS,5S,6R,7aR,7bS,9aS,10R,12aS,12bS)-10-[(2S,3R,4R,5S)-3,4-dihydroxy-5,6-dimethylheptan-2-yl]-5,6-dihydroxy-7a,9a-dime thylhexadecahydro-3H-benzo[c]indeno[5,4-e]oxepin-3-one


Mass: 480.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H48O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
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: BL-bound atABCB19 in lipid nanodisc / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.13679 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.8 / Details: 20mM Tris-HCl,pH 7.8, 150mM NaCl
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid 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 defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191000 / Symmetry type: POINT

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