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- EMDB-60369: Structure of the wild-type Arabidopsis ABCB1 in the brassinolide-... -

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Basic information

Entry
Database: EMDB / ID: EMD-60369
TitleStructure of the wild-type Arabidopsis ABCB1 in the brassinolide-bound state
Map data
Sample
  • Complex: Purified wild-type ABCB1 protein in complex with brassinolide
    • Protein or peptide: ABC transporter B family member 1
  • Ligand: Brassinolide
KeywordsABC transporter / wild-type / brassinolide-bound state / TRANSPORT PROTEIN
Function / homology
Function and homology information


auxin influx transmembrane transporter activity / anthocyanin accumulation in tissues in response to UV light / response to red or far red light / auxin export across the plasma membrane / stamen development / positive gravitropism / auxin efflux transmembrane transporter activity / auxin polar transport / response to blue light / photomorphogenesis ...auxin influx transmembrane transporter activity / anthocyanin accumulation in tissues in response to UV light / response to red or far red light / auxin export across the plasma membrane / stamen development / positive gravitropism / auxin efflux transmembrane transporter activity / auxin polar transport / response to blue light / photomorphogenesis / response to auxin / auxin-activated signaling pathway / plasmodesma / response to nematode / regulation of cell size / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / plasma membrane
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
ABC transporter B family member 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYing W / Wei H / Liu X / Sun L
Funding support China, 2 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37020103 China
National Natural Science Foundation of China (NSFC)32321001; 31900885; 32322041 China
CitationJournal: Plant Commun / Year: 2025
Title: Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1.
Authors: Hong Wei / Heyuan Zhu / Wei Ying / Hilde Janssens / Miroslav Kvasnica / Johan M Winne / Yongxiang Gao / Jiří Friml / Qian Ma / Shutang Tan / Xin Liu / Eugenia Russinova / Linfeng Sun /
Abstract: Brassinosteroids (BRs) are steroidal phytohormones indispensable for plant growth, development, and responses to environmental stresses. The export of bioactive BRs to the apoplast is essential for ...Brassinosteroids (BRs) are steroidal phytohormones indispensable for plant growth, development, and responses to environmental stresses. The export of bioactive BRs to the apoplast is essential for BR signaling initiation, which requires binding of a BR molecule to the extracellular domains of the plasma membrane-localized receptor complex. We have previously shown that the Arabidopsis thaliana ATP-binding cassette (ABC) transporter ABCB19 functions as a BR exporter and, together with its close homolog ABCB1, positively regulates BR signaling. Here, we demonstrate that ABCB1 is another BR transporter. The ATP hydrolysis activity of ABCB1 can be stimulated by bioactive BRs, and its transport activity was confirmed in proteoliposomes and protoplasts. Structures of ABCB1 were determined in substrate-unbound (apo), brassinolide (BL)-bound, and ATP plus BL-bound states. In the BL-bound structure, BL is bound to the hydrophobic cavity formed by the transmembrane domain and triggers local conformational changes. Together, our data provide additional insights into ABC transporter-mediated BR export.
History
DepositionMay 31, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60369.png

Downloads & links

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Map

FileDownload / File: emd_60369.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.370153 - 4.539189
Average (Standard dev.)-0.00041677986 (±0.09147579)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60369_msk_1.map
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Half map: Half map-1

Fileemd_60369_half_map_1.map
AnnotationHalf map-1
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Half map: Half map-2

Fileemd_60369_half_map_2.map
AnnotationHalf map-2
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Sample components

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Entire : Purified wild-type ABCB1 protein in complex with brassinolide

EntireName: Purified wild-type ABCB1 protein in complex with brassinolide
Components
  • Complex: Purified wild-type ABCB1 protein in complex with brassinolide
    • Protein or peptide: ABC transporter B family member 1
  • Ligand: Brassinolide

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Supramolecule #1: Purified wild-type ABCB1 protein in complex with brassinolide

SupramoleculeName: Purified wild-type ABCB1 protein in complex with brassinolide
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: ABC transporter B family member 1

MacromoleculeName: ABC transporter B family member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 140.729141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDNDGGAPPP PPTLVVEEPK KAEIRGVAFK ELFRFADGLD YVLMGIGSVG AFVHGCSLPL FLRFFADLVN SFGSNSNNVE KMMEEVLKY ALYFLVVGAA IWASSWAEIS CWMWSGERQT TKMRIKYLEA ALNQDIQFFD TEVRTSDVVF AINTDAVMVQ D AISEKLGN ...String:
MDNDGGAPPP PPTLVVEEPK KAEIRGVAFK ELFRFADGLD YVLMGIGSVG AFVHGCSLPL FLRFFADLVN SFGSNSNNVE KMMEEVLKY ALYFLVVGAA IWASSWAEIS CWMWSGERQT TKMRIKYLEA ALNQDIQFFD TEVRTSDVVF AINTDAVMVQ D AISEKLGN FIHYMATFVS GFIVGFTAVW QLALVTLAVV PLIAVIGGIH TTTLSKLSNK SQESLSQAGN IVEQTVVQIR VV MAFVGES RASQAYSSAL KIAQKLGYKT GLAKGMGLGA TYFVVFCCYA LLLWYGGYLV RHHLTNGGLA IATMFAVMIG GLA LGQSAP SMAAFAKAKV AAAKIFRIID HKPTIERNSE SGVELDSVTG LVELKNVDFS YPSRPDVKIL NNFCLSVPAG KTIA LVGSS GSGKSTVVSL IERFYDPNSG QVLLDGQDLK TLKLRWLRQQ IGLVSQEPAL FATSIKENIL LGRPDADQVE IEEAA RVAN AHSFIIKLPD GFDTQVGERG LQLSGGQKQR IAIARAMLKN PAILLLDEAT SALDSESEKL VQEALDRFMI GRTTLI IAH RLSTIRKADL VAVLQQGSVS EIGTHDELFS KGENGVYAKL IKMQEAAHET AMSNARKSSA RPSSARNSVS SPIMTRN SS YGRSPYSRRL SDFSTSDFSL SIDASSYPNY RNEKLAFKDQ ANSFWRLAKM NSPEWKYALL GSVGSVICGS LSAFFAYV L SAVLSVYYNP DHEYMIKQID KYCYLLIGLS SAALVFNTLQ HSFWDIVGEN LTKRVREKML SAVLKNEMAW FDQEENESA RIAARLALDA NNVRSAIGDR ISVIVQNTAL MLVACTAGFV LQWRLALVLV AVFPVVVAAT VLQKMFMTGF SGDLEAAHAK GTQLAGEAI ANVRTVAAFN SEAKIVRLYT ANLEPPLKRC FWKGQIAGSG YGVAQFCLYA SYALGLWYAS WLVKHGISDF S KTIRVFMV LMVSANGAAE TLTLAPDFIK GGQAMRSVFE LLDRKTEIEP DDPDTTPVPD RLRGEVELKH IDFSYPSRPD IQ IFRDLSL RARAGKTLAL VGPSGCGKSS VISLIQRFYE PSSGRVMIDG KDIRKYNLKA IRKHIAIVPQ EPCLFGTTIY ENI AYGHEC ATEAEIIQAA TLASAHKFIS ALPEGYKTYV GERGVQLSGG QKQRIAIARA LVRKAEIMLL DEATSALDAE SERS VQEAL DQACSGRTSI VVAHRLSTIR NAHVIAVIDD GKVAEQGSHS HLLKNHPDGI YARMIQLQRF THTQVIGMTS GSSSR VKED DA

UniProtKB: ABC transporter B family member 1

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Macromolecule #2: Brassinolide

MacromoleculeName: Brassinolide / type: ligand / ID: 2 / Number of copies: 1 / Formula: BLD
Molecular weightTheoretical: 480.677 Da
Chemical component information

ChemComp-BLD:
Brassinolide / hormone*YM

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 243268
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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