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- PDB-9j12: Structure of the wild-type AZG2 in Arabidopsis thaliana in the ap... -

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Basic information

Entry
Database: PDB / ID: 9j12
TitleStructure of the wild-type AZG2 in Arabidopsis thaliana in the apo state at pH 5.5
ComponentsAdenine/guanine permease AZG2
KeywordsTRANSPORT PROTEIN / Cytokinin transporter / AZG2 / plant hormone
Function / homology
Function and homology information


guanine nucleotide transmembrane transport / adenine nucleotide transmembrane transporter activity / adenine nucleotide transport / guanine transport / purine nucleobase transmembrane transporter activity / purine nucleobase transport / adenine transport / guanine nucleotide transmembrane transporter activity / membrane
Similarity search - Function
Azaguanine-like transporters / Nucleobase cation symporter 2 family / Permease family
Similarity search - Domain/homology
Adenine/guanine permease AZG2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSun, L. / Liu, X. / Wei, H. / Yang, Z. / Ying, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32322041, 32321001, 31900885 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of cytokinin transport by the Arabidopsis AZG2.
Authors: Hong Wei / Zhisen Yang / Huihui Liu / Wei Ying / Yongxiang Gao / Lizhe Zhu / Xin Liu / Linfeng Sun /
Abstract: Cytokinins are adenine derivatives serving as phytohormones, which are essential regulators of plant growth, development, and response to environmental factors. The transport process of cytokinins ...Cytokinins are adenine derivatives serving as phytohormones, which are essential regulators of plant growth, development, and response to environmental factors. The transport process of cytokinins determines their spatial distributions and is critical to their functions. The AZA-GUANINE RESISTANT (AZG) family member AZG2 in Arabidopsis thaliana has been identified as a cytokinin and purine transporter. Here, we characterize the binding and transport of AZG2 towards the natural cytokinin, trans-zeatin (tZ), as well as adenine. AZG2 structures are determined in both the substrate-unbound, adenine-bound, and tZ-bound states, under both acidic and neutral pH. Key residues involved in substrate binding are identified. Two distinct conformations are observed in the tZ-bound state of AZG2 in the neutral pH. Structural analysis reveals the structural dynamics of AZG2 during cytokinin transport, which fit into the elevator-type transport model. These results provide insights into the molecular mechanism of cytokinin transport in plants.
History
DepositionAug 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 19, 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

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Assembly

Deposited unit
A: Adenine/guanine permease AZG2
B: Adenine/guanine permease AZG2


Theoretical massNumber of molelcules
Total (without water)112,6452
Polymers112,6452
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 Adenine/guanine permease AZG2 / AzgA-homolog protein / Protein AZAGUANINE RESISTANT 2 / AtAzg2


Mass: 56322.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AZG2, At5g50300, K6A12.16 / Production host: Homo sapiens (human) / Strain (production host): HEK293F / References: UniProt: Q84MA8
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: AZG2 dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 5.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30031 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037593
ELECTRON MICROSCOPYf_angle_d0.74310323
ELECTRON MICROSCOPYf_dihedral_angle_d4.7291061
ELECTRON MICROSCOPYf_chiral_restr0.0431250
ELECTRON MICROSCOPYf_plane_restr0.0061270

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