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- EMDB-61830: Structure of Arabidopsis thaliana ABCB1 with brassinolide and AMP... -

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Basic information

Entry
Database: EMDB / ID: EMD-61830
TitleStructure of Arabidopsis thaliana ABCB1 with brassinolide and AMP-PNP bound in the inward-facing conformation
Map data
Sample
  • Complex: Structure of Arabidopsis thaliana ABCB1 with brassinolide and AMP-PNP bound in the inward-facing conformation
    • Protein or peptide: ABC transporter B family member 1
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: Brassinolide
KeywordsABCB1 / auxin transport / brassinolide (BL) transport / 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: 3.1 Å
AuthorsChen Q / Su N / Guo J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32400995 China
CitationJournal: Structure / Year: 2025
Title: Structures and mechanisms of the ABC transporter ABCB1 from Arabidopsis thaliana.
Authors: Qian Chen / Li Zhu / Sufen Zhang / Shuai Qiao / Zhong Jie Ding / Shao Jian Zheng / Jiangtao Guo / Nannan Su /
Abstract: The Arabidopsis thaliana auxin transporter ABCB1 plays a fundamental role in the regulation of plant growth and development. While its homolog ABCB19 was previously shown to transport ...The Arabidopsis thaliana auxin transporter ABCB1 plays a fundamental role in the regulation of plant growth and development. While its homolog ABCB19 was previously shown to transport brassinosteroids (BR), another class of essential hormones, the ability of ABCB1 to mediate BR transport has remained unexplored. In this study we show that ABCB1 also transports brassinosteroids with an in vitro brassinolide (BL) transport assay. Using single-particle cryo-electron microscopy, we determined ABCB1 structures in multiple inward-facing conformations in the apo state, ANP-bound state, BL-bound state, and the both BL- and ANP-bound state. BL binds to the large cavity of two transmembrane domains, inducing a slight conformational change. Additionally, we obtained the structure of ABCB1 in an outward-facing conformation. By comparing these different conformations, we elucidated the possible mechanism of hormone transport by ABCB1. These high-resolution structures help us to understand the structural basis for hormone recognition and transport mechanisms of ABCB1.
History
DepositionOct 8, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61830.png

Downloads & links

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Map

FileDownload / File: emd_61830.map.gz / Format: CCP4 / Size: 52.7 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.)
0.93 Å/pix.
x 240 pix.
= 223.2 Å		0.93 Å/pix.
x 240 pix.
= 223.2 Å		0.93 Å/pix.
x 240 pix.
= 223.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.020954343 - 0.053177163
Average (Standard dev.)0.0000034049467 (±0.0018876252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 223.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61830_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61830_half_map_2.map
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Sample components

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Entire : Structure of Arabidopsis thaliana ABCB1 with brassinolide and AMP...

EntireName: Structure of Arabidopsis thaliana ABCB1 with brassinolide and AMP-PNP bound in the inward-facing conformation
Components
  • Complex: Structure of Arabidopsis thaliana ABCB1 with brassinolide and AMP-PNP bound in the inward-facing conformation
    • Protein or peptide: ABC transporter B family member 1
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: Brassinolide

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Supramolecule #1: Structure of Arabidopsis thaliana ABCB1 with brassinolide and AMP...

SupramoleculeName: Structure of Arabidopsis thaliana ABCB1 with brassinolide and AMP-PNP bound in the inward-facing conformation
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: 145.318953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKW SHPQFEKGGG GSGGSAWSHP QFEKEFKGLV DMDNDGGAPP PPPTLVVEEP KKAEIRGVAF KELFRFADGL DYVLMGIGS VGAFVHGCSL PLFLRFFADL VNSFGSNSNN VEKMMEEVLK YALYFLVVGA AIWASSWAEI SCWMWSGERQ T TKMRIKYL ...String:
MDYKDDDDKW SHPQFEKGGG GSGGSAWSHP QFEKEFKGLV DMDNDGGAPP PPPTLVVEEP KKAEIRGVAF KELFRFADGL DYVLMGIGS VGAFVHGCSL PLFLRFFADL VNSFGSNSNN VEKMMEEVLK YALYFLVVGA AIWASSWAEI SCWMWSGERQ T TKMRIKYL EAALNQDIQF FDTEVRTSDV VFAINTDAVM VQDAISEKLG NFIHYMATFV SGFIVGFTAV WQLALVTLAV VP LIAVIGG IHTTTLSKLS NKSQESLSQA GNIVEQTVVQ IRVVMAFVGE SRASQAYSSA LKIAQKLGYK TGLAKGMGLG ATY FVVFCC YALLLWYGGY LVRHHLTNGG LAIATMFAVM IGGLALGQSA PSMAAFAKAK VAAAKIFRII DHKPTIERNS ESGV ELDSV TGLVELKNVD FSYPSRPDVK ILNNFCLSVP AGKTIALVGS SGSGKSTVVS LIERFYDPNS GQVLLDGQDL KTLKL RWLR QQIGLVSQEP ALFATSIKEN ILLGRPDADQ VEIEEAARVA NAHSFIIKLP DGFDTQVGER GLQLSGGQKQ RIAIAR AML KNPAILLLDE ATSALDSESE KLVQEALDRF MIGRTTLIIA HRLSTIRKAD LVAVLQQGSV SEIGTHDELF SKGENGV YA KLIKMQEAAH ETAMSNARKS SARPSSARNS VSSPIMTRNS SYGRSPYSRR LSDFSTSDFS LSIDASSYPN YRNEKLAF K DQANSFWRLA KMNSPEWKYA LLGSVGSVIC GSLSAFFAYV LSAVLSVYYN PDHEYMIKQI DKYCYLLIGL SSAALVFNT LQHSFWDIVG ENLTKRVREK MLSAVLKNEM AWFDQEENES ARIAARLALD ANNVRSAIGD RISVIVQNTA LMLVACTAGF VLQWRLALV LVAVFPVVVA ATVLQKMFMT GFSGDLEAAH AKGTQLAGEA IANVRTVAAF NSEAKIVRLY TANLEPPLKR C FWKGQIAG SGYGVAQFCL YASYALGLWY ASWLVKHGIS DFSKTIRVFM VLMVSANGAA ETLTLAPDFI KGGQAMRSVF EL LDRKTEI EPDDPDTTPV PDRLRGEVEL KHIDFSYPSR PDIQIFRDLS LRARAGKTLA LVGPSGCGKS SVISLIQRFY EPS SGRVMI DGKDIRKYNL KAIRKHIAIV PQEPCLFGTT IYENIAYGHE CATEAEIIQA ATLASAHKFI SALPEGYKTY VGER GVQLS GGQKQRIAIA RALVRKAEIM LLDEATSALD AESERSVQEA LDQACSGRTS IVVAHRLSTI RNAHVIAVID DGKVA EQGS HSHLLKNHPD GIYARMIQLQ RFTHTQVIGM TSGSSSRVKE DDA

UniProtKB: ABC transporter B family member 1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #4: Brassinolide

MacromoleculeName: Brassinolide / type: ligand / ID: 4 / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average exposure time: 3.42 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105302
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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