[English] 日本語
Yorodumi
- EMDB-37705: Structure of the Arabidopsis E529Q/E1174Q ABCB19 in the ATP bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37705
TitleStructure of the Arabidopsis E529Q/E1174Q ABCB19 in the ATP bound state
Map data
Sample
  • Organelle or cellular component: Purified E529Q/E1174Q mutant ABCB19 protein in complex with ATP
    • Protein or peptide: ABC transporter B family member 19
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsABC transporter / 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 / positive regulation of brassinosteroid mediated signaling pathway / response to red or far red light / lateral root development / stamen development / response to brassinosteroid ...acropetal auxin transport / formation of plant organ boundary / basipetal auxin transport / auxin transport / anthocyanin accumulation in tissues in response to UV light / positive regulation of brassinosteroid mediated signaling pathway / response to red or far red light / lateral root development / stamen development / response to brassinosteroid / positive gravitropism / auxin export across the plasma membrane / auxin efflux transmembrane transporter activity / auxin polar transport / response to far red light / root development / photomorphogenesis / response to auxin / response to blue light / 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 8, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37705.png

Downloads & links

-
Map

FileDownload / File: emd_37705.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.9577303 - 5.0046544
Average (Standard dev.)0.005259961 (±0.104753405)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_37705_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37705_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Purified E529Q/E1174Q mutant ABCB19 protein in complex with ATP

EntireName: Purified E529Q/E1174Q mutant ABCB19 protein in complex with ATP
Components
  • Organelle or cellular component: Purified E529Q/E1174Q mutant ABCB19 protein in complex with ATP
    • Protein or peptide: ABC transporter B family member 19
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Purified E529Q/E1174Q mutant ABCB19 protein in complex with ATP

SupramoleculeName: Purified E529Q/E1174Q mutant ABCB19 protein in complex with ATP
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
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: 136.930594 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 LLLDQATSAL 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 PTVLLLDQAT SALDAESECV LQEALERLMR GRTT VVVAH RLSTIRGVDC IGVIQDGRIV EQGSHSELVS RPEGAYSRLL QLQTHRI

UniProtKB: ABC transporter B family member 19

-
Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: NONE
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: 398664
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more