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- EMDB-63418: IAA-free AUX1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63418
TitleIAA-free AUX1
Map data
Sample
  • Complex: AUX1
    • Protein or peptide: Auxin transporter protein 1,Soluble cytochrome b562
    • Protein or peptide: heavy chain
    • Protein or peptide: Nanobody
    • Protein or peptide: light chain
KeywordsLeuT-fold / transport / PROTEIN TRANSPORT/IMMUNE SYSTEM / PROTEIN TRANSPORT-IMMUNE SYSTEM complex
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 / electron transport chain / periplasmic space / electron transfer activity / endosome / iron ion binding / heme binding / cell surface / Golgi apparatus / plasma membrane
Similarity search - Function
Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Soluble cytochrome b562 / Auxin transporter protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Homo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsJing D / Kong F / Wang CC / Shi YG / Huang GXY
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Structural basis of auxin binding and transport by Arabidopsis thaliana AUX1
Authors: Jing D / Kong F
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_63418.png

Downloads & links

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Map

FileDownload / File: emd_63418.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 344.736 Å		1.08 Å/pix.
x 320 pix.
= 344.736 Å		1.08 Å/pix.
x 320 pix.
= 344.736 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: 0.4
Minimum - Maximum-4.2827363 - 7.65236
Average (Standard dev.)0.0007432045 (±0.0590062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 344.736 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63418_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63418_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63418_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,Soluble cytochrome b562
    • Protein or peptide: heavy chain
    • Protein or peptide: Nanobody
    • Protein or peptide: light chain

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Supramolecule #1: AUX1

SupramoleculeName: AUX1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4, #3
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Auxin transporter protein 1,Soluble cytochrome b562

MacromoleculeName: Auxin transporter protein 1,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 68.898891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHH HGSVEDYKDD DDKGSMSEGV EAIVANDNGT DQVNGNRTGK DNEEHDGSTG SNLSNFLWHG GSVWDAWFSC ASNQVAQVL LTLPYSFSQL GMLSGIVLQI FYGLLGSWTA YLISVLYVEY RARKEKEGKS FKADLEDNWE TLNDNLKVIE K ADNAAQVK ...String:
MHHHHHHHHH HGSVEDYKDD DDKGSMSEGV EAIVANDNGT DQVNGNRTGK DNEEHDGSTG SNLSNFLWHG GSVWDAWFSC ASNQVAQVL LTLPYSFSQL GMLSGIVLQI FYGLLGSWTA YLISVLYVEY RARKEKEGKS FKADLEDNWE TLNDNLKVIE K ADNAAQVK DALTKMRAAA LDAQKATPPK LEDKSPDSPE MKDFRHGFDI LVGQIDDALK LANEGKVKEA QAAAEQLKTT RN AYIQKYL NHVIQWFEVL DGLLGSYWKA LGLAFNCTFL LFGSVIQLIA CASNIYYIND HLDKRTWTYI FGACCATTVF IPS FHNYRI WSFLGLGMTT YTAWYLAIAS IIHGQAEGVK HSGPTKLVLY FTGATNILYT FGGHAVTVEI MHAMWKPQKF KYIY LMATL YVFTLTIPSA AAVYWAFGDA LLDHSNAFSL MPKNAWRDAA VILMLIHQFI TFGFACTPLY FVWEKVIGMH DTKSI CLRA LARLPVVIPI WFLAIIFPFF GPINSAVGAL LVSFTVYIIP SLAHMLTYRS ASARQNAAEK PPFFMPSWTA MYVLNA FVV VWVLIVGFGF GGWASVTNFV RQVDTFGLFA KCYQCKPAAA AAHAPVSALH HRL

UniProtKB: Auxin transporter protein 1, Soluble cytochrome b562, Auxin transporter protein 1

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Macromolecule #2: heavy chain

MacromoleculeName: heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.569965 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSLILLFL VAVATRVLSE ISEVQLVESG GGLVQPGGSL RLSCAASGFN VVDFSLHWVR QAPGKGLEWV AYISSSSGST SYADSVKGR FTISADTSKN TAYLQMNSLR AEDTAVYYCA RWGYWPGEPW WKAFDYWGQG TLVTVSSAST KGPSVFPLAP S SKSTSGGT ...String:
MGWSLILLFL VAVATRVLSE ISEVQLVESG GGLVQPGGSL RLSCAASGFN VVDFSLHWVR QAPGKGLEWV AYISSSSGST SYADSVKGR FTISADTSKN TAYLQMNSLR AEDTAVYYCA RWGYWPGEPW WKAFDYWGQG TLVTVSSAST KGPSVFPLAP S SKSTSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KV DKKVEPK SCDKHHHHHH

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Macromolecule #3: light chain

MacromoleculeName: light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.575604 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSS DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGT DFTLTISSLQ PEDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN F YPREAKVQ ...String:
MGWSCIILFL VATATGVHSS DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGT DFTLTISSLQ PEDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 19.229166 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSQVQLQE SGGGLVQPGG SLRLSCAASG RTISRYAMSW FRQAPGKERE FVAVARRSG DGAFYADSVQ GRFTVSRDDA KNTVYLQMNS LKPEDTAVYY CAIDSDTFYS GSYDYWGQGT QVTVSSLEHH H HHHGSDYK DDDDK

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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: 1.6 µm / Nominal defocus min: 1.2 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 / Details: AF-Q96247-F1
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 175799
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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