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- PDB-8jh5: Structure of the auxin exporter PIN1 in Arabidopsis thaliana in t... -

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Basic information

Entry
Database: PDB / ID: 8jh5
TitleStructure of the auxin exporter PIN1 in Arabidopsis thaliana in the Naproxen-bound state
Components
  • Auxin efflux carrier component 1
  • nanobody
KeywordsPLANT PROTEIN / membrane transporter
Function / homology
Function and homology information


cotyledon morphogenesis / leaf formation / cotyledon development / shoot system development / leaf shaping / xylem and phloem pattern formation / auxin efflux transmembrane transporter activity / inflorescence development / auxin polar transport / gravitropism ...cotyledon morphogenesis / leaf formation / cotyledon development / shoot system development / leaf shaping / xylem and phloem pattern formation / auxin efflux transmembrane transporter activity / inflorescence development / auxin polar transport / gravitropism / plant-type cell wall / photomorphogenesis / root development / flower development / auxin-activated signaling pathway / embryo development ending in seed dormancy / plasmodesma / basal plasma membrane / apical part of cell / plasma membrane / cytoplasm
Similarity search - Function
Membrane transport protein / Auxin efflux carrier, plant type / Membrane transport protein
Similarity search - Domain/homology
(2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid / Auxin efflux carrier component 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSun, L. / Liu, X. / Yang, Z. / Xia, J.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37020103 China
National Natural Science Foundation of China (NSFC)31900885 China
National Natural Science Foundation of China (NSFC)31870732 China
CitationJournal: To be published
Title: Structure of the auxin exporter PIN1 in Arabidopsis thaliana in the Naproxen-bound state
Authors: Sun, L. / Liu, X. / Yang, Z. / Xia, J.
History
DepositionMay 22, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Auxin efflux carrier component 1
C: nanobody
D: nanobody
B: Auxin efflux carrier component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,2986
Polymers160,8374
Non-polymers4612
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 efflux carrier component 1 / Protein PIN-FORMED / AtPIN1


Mass: 67080.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PIN1, At1g73590, F6D5.2 / Plasmid: pCAG / Production host: Homo sapiens (human) / Strain (production host): HEK293F / References: UniProt: Q9C6B8
#2: Antibody nanobody


Mass: 13337.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-NPS / (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid / NAPROXEN


Mass: 230.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory*YM
Has ligand of interestY

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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: Binary complex of PIN1 with nanobody / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal defocus max: 2300 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48551 / Symmetry type: POINT

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