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- PDB-9lvb: IAA-free AUX1 -

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Basic information

Entry
Database: PDB / ID: 9lvb
TitleIAA-free AUX1
Components
  • Auxin transporter protein 1,Soluble cytochrome b562
  • Nanobody
  • heavy chain
  • light chain
KeywordsPROTEIN TRANSPORT/IMMUNE SYSTEM / LeuT-fold / transport / PROTEIN TRANSPORT-IMMUNE SYSTEM complex
Function / homology
Function and homology information


root hair cell differentiation / auxin binding / root cap development / lateral root formation / auxin influx transmembrane transporter activity / positive gravitropism / establishment of planar polarity / auxin polar transport / auxin-activated signaling pathway / symporter activity ...root hair cell differentiation / auxin binding / root cap development / lateral root formation / auxin influx transmembrane transporter activity / positive gravitropism / establishment of planar polarity / auxin polar transport / auxin-activated signaling pathway / symporter activity / amino acid transmembrane transporter 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)
Escherichia coli (E. coli)
Homo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsJing, D. / Kong, F. / Wang, C.C. / Shi, Y.G. / Huang, G.X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis of auxin binding and transport by AUX1.
Authors: Dan Jing / Fang Kong / Xiaoli Lu / Gaoxingyu Huang / Jing Huang / Haolin Wang / Yigong Shi / Chengcheng Wang /
Abstract: Indole-3-acetic acid (IAA), the major form of auxin, is essential for plant growth. Auxin resistant 1 (AUX1), the first identified auxin importer, plays a crucial role in polar auxin transport (PAT). ...Indole-3-acetic acid (IAA), the major form of auxin, is essential for plant growth. Auxin resistant 1 (AUX1), the first identified auxin importer, plays a crucial role in polar auxin transport (PAT). Here, we present cryo-EM structures of AUX1 in the IAA-free and IAA-bound states. AUX1 exists as a monomer that contains 11 transmembrane helices (TMs). TMs 1 to 5 and 6 to 10 constitute the two halves of a classic LeuT-fold, and TM11 interacts with both halves at the interface. In the IAA-bound state, IAA is specifically recognized in a central pocket formed by TM1, TM3, TM6, and TM8. In the presence of IAA, TM1 and TM6 undergo marked conformational changes that are critical for IAA transport. His249 stands out to be a key residue for substrate uptake and release. Our structures reveal the molecular basis for AUX1-mediated IAA binding and transport.
History
DepositionFeb 12, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Auxin transporter protein 1,Soluble cytochrome b562
H: heavy chain
L: light chain
N: Nanobody


Theoretical massNumber of molelcules
Total (without water)141,2744
Polymers141,2744
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 68898.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress), (gene. exp.) Escherichia coli (E. coli)
Gene: AUX1, cybC / Production host: Homo sapiens (human) / References: UniProt: Q96247, UniProt: P0ABE7
#2: Antibody heavy chain


Mass: 27569.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody light chain


Mass: 25575.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Nanobody


Mass: 19229.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: AUX1 / Type: COMPLEX / Entity ID: #1-#2, #4, #3 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Arabidopsis thaliana (thale cress)3702
21Homo sapiens (human)9606
31Escherichia coli (E. coli)562
41Lama glama (llama)9844
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: LMNG/CHS
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175799 / Symmetry type: POINT
RefinementHighest resolution: 3.97 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037504
ELECTRON MICROSCOPYf_angle_d0.52210223
ELECTRON MICROSCOPYf_dihedral_angle_d4.3771009
ELECTRON MICROSCOPYf_chiral_restr0.0381147
ELECTRON MICROSCOPYf_plane_restr0.0031276

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