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- EMDB-63417: IAA-bound AUX1 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63417
TitleIAA-bound AUX1
Map data
Sample
  • Complex: AUX1
    • Protein or peptide: Auxin transporter protein 1
  • Ligand: 1H-INDOL-3-YLACETIC ACID
Keywordstransport / LeuT-fold / PROTEIN TRANSPORT
Function / homology
Function and homology information


root hair cell differentiation / root cap development / auxin binding / lateral root formation / auxin influx transmembrane transporter activity / positive gravitropism / auxin polar transport / establishment of planar polarity / auxin-activated signaling pathway / amino acid transmembrane transporter activity ...root hair cell differentiation / root cap development / auxin binding / lateral root formation / auxin influx transmembrane transporter activity / positive gravitropism / auxin polar transport / establishment of planar polarity / auxin-activated signaling pathway / amino acid transmembrane transporter activity / symporter activity / response to nematode / endosome / cell surface / Golgi apparatus / plasma membrane
Similarity search - Function
Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein
Similarity search - Domain/homology
Auxin transporter protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsWang CC / Jing D / Kong F / Huang GXY / Shi YG
Funding support1 items
OrganizationGrant numberCountry
Other government2020C04001
CitationJournal: To Be Published
Title: Structural basis of auxin binding and transport by Arabidopsis thaliana AUX1
Authors: Jing D / Kong F / Shi YG / Huang GXY / Wang CC
History
DepositionFeb 12, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63417.png

Downloads & links

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Map

FileDownload / File: emd_63417.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 192 pix.
= 206.842 Å		1.08 Å/pix.
x 192 pix.
= 206.842 Å		1.08 Å/pix.
x 192 pix.
= 206.842 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-9.684945000000001 - 16.859317999999998
Average (Standard dev.)0.0013421454 (±0.15661648)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 206.84158 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63417_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63417_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63417_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AUX1

EntireName: AUX1
Components
  • Complex: AUX1
    • Protein or peptide: Auxin transporter protein 1
  • Ligand: 1H-INDOL-3-YLACETIC ACID

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Supramolecule #1: AUX1

SupramoleculeName: AUX1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Auxin transporter protein 1

MacromoleculeName: Auxin transporter protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 57.131629 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHH HGSVEDYKDD DDKGSMSEGV EAIVANDNGT DQVNGNRTGK DNEEHDGSTG SNLSNFLWHG GSVWDAWFSC ASNQVAQVL LTLPYSFSQL GMLSGIVLQI FYGLLGSWTA YLISVLYVEY RARKEKEGKS FKNHVIQWFE VLDGLLGSYW K ALGLAFNC ...String:
MHHHHHHHHH HGSVEDYKDD DDKGSMSEGV EAIVANDNGT DQVNGNRTGK DNEEHDGSTG SNLSNFLWHG GSVWDAWFSC ASNQVAQVL LTLPYSFSQL GMLSGIVLQI FYGLLGSWTA YLISVLYVEY RARKEKEGKS FKNHVIQWFE VLDGLLGSYW K ALGLAFNC TFLLFGSVIQ LIACASNIYY INDHLDKRTW TYIFGACCAT TVFIPSFHNY RIWSFLGLGM TTYTAWYLAI AS IIHGQAE GVKHSGPTKL VLYFTGATNI LYTFGGHAVT VEIMHAMWKP QKFKYIYLMA TLYVFTLTIP SAAAVYWAFG DAL LDHSNA FSLMPKNAWR DAAVILMLIH QFITFGFACT PLYFVWEKVI GMHDTKSICL RALARLPVVI PIWFLAIIFP FFGP INSAV GALLVSFTVY IIPSLAHMLT YRSASARQNA AEKPPFFMPS WTAMYVLNAF VVVWVLIVGF GFGGWASVTN FVRQV DTFG LFAKCYQCKP AAAAAHAPVS ALHHRL

UniProtKB: Auxin transporter protein 1

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Macromolecule #2: 1H-INDOL-3-YLACETIC ACID

MacromoleculeName: 1H-INDOL-3-YLACETIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: IAC
Molecular weightTheoretical: 175.184 Da
Chemical component information

ChemComp-IAC:
1H-INDOL-3-YLACETIC ACID / 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
Sugar embeddingMaterial: LMNG/CHS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131289
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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