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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 / 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)
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: To Be Published
Title: Structural basis of auxin binding and transport by Arabidopsis thaliana AUX1
Authors: Jing, D. / Kong, F.
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
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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