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- EMDB-37690: Structure of the wild-type Arabidopsis ABCB19 in the apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-37690
TitleStructure of the wild-type Arabidopsis ABCB19 in the apo state
Map data
Sample
  • Organelle or cellular component: Purified wild-type ABCB19 protein
    • Protein or peptide: ABC transporter B family member 19
KeywordsABC transporter / wild-type / apo state / TRANSPORT PROTEIN
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
ABC transporter B family member 19
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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)31900885; 31870732; 32322041 China
CitationJournal: Science / Year: 2024
Title: Structure and function of the ABC transporter ABCB19 in brassinosteroid export.
Authors: Wei Ying / Yaowei Wang / Hong Wei / Yongming Luo / Qian Ma / Heyuan Zhu / Hilde Janssens / Nemanja Vukašinović / Miroslav Kvasnica / Johan M Winne / Yongxiang Gao / Shutang Tan / Jiří ...Authors: Wei Ying / Yaowei Wang / Hong Wei / Yongming Luo / Qian Ma / Heyuan Zhu / Hilde Janssens / Nemanja Vukašinović / Miroslav Kvasnica / Johan M Winne / Yongxiang Gao / Shutang Tan / Jiří Friml / Xin Liu / Eugenia Russinova / Linfeng Sun /
Abstract: Brassinosteroids are steroidal phytohormones that regulate plant development and physiology, including adaptation to environmental stresses. Brassinosteroids are synthesized in the cell interior but ...Brassinosteroids are steroidal phytohormones that regulate plant development and physiology, including adaptation to environmental stresses. Brassinosteroids are synthesized in the cell interior but bind receptors at the cell surface, necessitating a yet to be identified export mechanism. Here, we show that a member of the ATP-binding cassette (ABC) transporter superfamily, ABCB19, functions as a brassinosteroid exporter. We present its structure in both the substrate-unbound and the brassinosteroid-bound states. Bioactive brassinosteroids are potent activators of ABCB19 ATP hydrolysis activity, and transport assays showed that ABCB19 transports brassinosteroids. In , ABCB19 and its close homolog, ABCB1, positively regulate brassinosteroid responses. Our results uncover an elusive export mechanism for bioactive brassinosteroids that is tightly coordinated with brassinosteroid signaling.
History
DepositionOct 7, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37690.png

Downloads & links

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Map

FileDownload / File: emd_37690.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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Others
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 (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.8656514 - 4.617472
Average (Standard dev.)0.0033573397 (±0.09955822)
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_37690_msk_1.map
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Half map: #2

Fileemd_37690_half_map_1.map
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Half map: #1

Fileemd_37690_half_map_2.map
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Sample components

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Entire : Purified wild-type ABCB19 protein

EntireName: Purified wild-type ABCB19 protein
Components
  • Organelle or cellular component: Purified wild-type ABCB19 protein
    • Protein or peptide: ABC transporter B family member 19

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Supramolecule #1: Purified wild-type ABCB19 protein

SupramoleculeName: Purified wild-type ABCB19 protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: ABC transporter B family member 19

MacromoleculeName: ABC transporter B family member 19 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 136.932562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSETNTTDAK TVPAEAEKKK EQSLPFFKLF SFADKFDYLL MFVGSLGAIV HGSSMPVFFL LFGQMVNGFG KNQMDLHQMV HEVSRYSLY FVYLGLVVCF SSYAEIACWM YSGERQVAAL RKKYLEAVLK QDVGFFDTDA RTGDIVFSVS TDTLLVQDAI S EKVGNFIH ...String:
MSETNTTDAK TVPAEAEKKK EQSLPFFKLF SFADKFDYLL MFVGSLGAIV HGSSMPVFFL LFGQMVNGFG KNQMDLHQMV HEVSRYSLY FVYLGLVVCF SSYAEIACWM YSGERQVAAL RKKYLEAVLK QDVGFFDTDA RTGDIVFSVS TDTLLVQDAI S EKVGNFIH YLSTFLAGLV VGFVSAWKLA LLSVAVIPGI AFAGGLYAYT LTGITSKSRE SYANAGVIAE QAIAQVRTVY SY VGESKAL NAYSDAIQYT LKLGYKAGMA KGLGLGCTYG IACMSWALVF WYAGVFIRNG QTDGGKAFTA IFSAIVGGMS LGQ SFSNLG AFSKGKAAGY KLMEIINQRP TIIQDPLDGK CLDQVHGNIE FKDVTFSYPS RPDVMIFRNF NIFFPSGKTV AVVG GSGSG KSTVVSLIER FYDPNSGQIL LDGVEIKTLQ LKFLREQIGL VNQEPALFAT TILENILYGK PDATMVEVEA AASAA NAHS FITLLPKGYD TQVGERGVQL SGGQKQRIAI ARAMLKDPKI LLLDEATSAL DASSESIVQE ALDRVMVGRT TVVVAH RLC TIRNVDSIAV IQQGQVVETG THEELIAKSG AYASLIRFQE MVGTRDFSNP STRRTRSTRL SHSLSTKSLS LRSGSLR NL SYSYSTGADG RIEMISNAET DRKTRAPENY FYRLLKLNSP EWPYSIMGAV GSILSGFIGP TFAIVMSNMI EVFYYTDY D SMERKTKEYV FIYIGAGLYA VGAYLIQHYF FSIMGENLTT RVRRMMLSAI LRNEVGWFDE DEHNSSLIAA RLATDAADV KSAIAERISV ILQNMTSLLT SFIVAFIVEW RVSLLILGTF PLLVLANFAQ QLSLKGFAGD TAKAHAKTSM IAGEGVSNIR TVAAFNAQS KILSLFCHEL RVPQKRSLYR SQTSGFLFGL SQLALYGSEA LILWYGAHLV SKGVSTFSKV IKVFVVLVIT A NSVAETVS LAPEIIRGGE AVGSVFSVLD RQTRIDPDDA DADPVETIRG DIEFRHVDFA YPSRPDVMVF RDFNLRIRAG HS QALVGAS GSGKSSVIAM IERFYDPLAG KVMIDGKDIR RLNLKSLRLK IGLVQQEPAL FAATIFDNIA YGKDGATESE VID AARAAN AHGFISGLPE GYKTPVGERG VQLSGGQKQR IAIARAVLKN PTVLLLDEAT SALDAESECV LQEALERLMR GRTT VVVAH RLSTIRGVDC IGVIQDGRIV EQGSHSELVS RPEGAYSRLL QLQTHRI

UniProtKB: ABC transporter B family member 19

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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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 437211
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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