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- EMDB-62383: Cryo-EM structure of vanadate-trapped atABCB19 in lipid nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-62383
TitleCryo-EM structure of vanadate-trapped atABCB19 in lipid nanodisc
Map data
Sample
  • Complex: vanadate-trapped atABCB19 in lipid nanodisc
    • Protein or peptide: ABC transporter B family member 19
  • Ligand: VANADATE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsABCB19 / Plant hormone transport / vandate-trapped / MEMBRANE 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: 3.7 Å
AuthorsLiu Y / Liao M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of vanadate-trapped atABCB19 in lipid nanodisc
Authors: Liu Y
History
DepositionNov 12, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62383.png

Downloads & links

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Map

FileDownload / File: emd_62383.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.)
0.86 Å/pix.
x 256 pix.
= 218.88 Å		0.86 Å/pix.
x 256 pix.
= 218.88 Å		0.86 Å/pix.
x 256 pix.
= 218.88 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.050419047 - 0.08912328
Average (Standard dev.)0.0000011729162 (±0.0029548628)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 218.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62383_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_62383_half_map_1.map
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Histogram

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Half map: #1

Fileemd_62383_half_map_2.map
Projections & Slices
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Sample components

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Entire : vanadate-trapped atABCB19 in lipid nanodisc

EntireName: vanadate-trapped atABCB19 in lipid nanodisc
Components
  • Complex: vanadate-trapped atABCB19 in lipid nanodisc
    • Protein or peptide: ABC transporter B family member 19
  • Ligand: VANADATE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: vanadate-trapped atABCB19 in lipid nanodisc

SupramoleculeName: vanadate-trapped atABCB19 in lipid nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 136.79 KDa

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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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Macromolecule #2: VANADATE ION

MacromoleculeName: VANADATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: VO4
Molecular weightTheoretical: 114.939 Da
Chemical component information

ChemComp-VN3:
VANADATE ION

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration2.0 mg/mL
BufferpH: 7.8 / Details: 20mM Tris-HCl,pH 7.8, 150mM NaCl
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58202
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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