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- EMDB-61066: Structure of the wild-type AZG2 in Arabidopsis thaliana in the ap... -

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Basic information

Entry
Database: EMDB / ID: EMD-61066
TitleStructure of the wild-type AZG2 in Arabidopsis thaliana in the apo state at pH 7.4
Map data
Sample
  • Complex: AZG2 dimer
    • Protein or peptide: Adenine/guanine permease AZG2
KeywordsCytokinin transporter / AZG2 / plant hormone / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSun L / Liu X / Wei H / Yang Z / Ying W
Funding support China, 1 items
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, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61066.png

Downloads & links

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Map

FileDownload / File: emd_61066.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-1.188973 - 1.5348375
Average (Standard dev.)0.0024381536 (±0.042425603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61066_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_61066_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_61066_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : AZG2 dimer

EntireName: AZG2 dimer
Components
  • Complex: AZG2 dimer
    • Protein or peptide: Adenine/guanine permease AZG2

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Supramolecule #1: AZG2 dimer

SupramoleculeName: AZG2 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Adenine/guanine permease AZG2

MacromoleculeName: Adenine/guanine permease AZG2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 56.322609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGREKTLCKS WSDMKKHLND TVSKSFIGRF FKLEARKTTF TTELRAATAT FLTMAYIITV NANILADSGA TCSINDCSTV ASSSPPGPE CVLGSNPGYE QCISRVKKDL VVATSLSAMV GSLAMGLLAN LPFGLAPGMG ANAYIAYNVV GFRGSGSISY H TAMAIVLL ...String:
MGREKTLCKS WSDMKKHLND TVSKSFIGRF FKLEARKTTF TTELRAATAT FLTMAYIITV NANILADSGA TCSINDCSTV ASSSPPGPE CVLGSNPGYE QCISRVKKDL VVATSLSAMV GSLAMGLLAN LPFGLAPGMG ANAYIAYNVV GFRGSGSISY H TAMAIVLL EGCAFLAVSA LGLRGKLARL IPQTVRLACA VGIGMFIAFV GLQMNQGIGL VGPDKSTLVT LTACAETDPV TG ACLGGKM KSPTFWLAVV GFLITSFGLM KNVKGSMIYG IVFVTAISWI RGTQVTIFPH TPLGDSNYNY FTKIVDFHKI QST LGAISF TEFRKSEVWV AFATLFYVDL LGTTGVLYTM AEIGGFVEDG KFEGEYAAYL VDAGSSVVGS ALGVTTTATF VESS AGLKE GGKTGLTAVI VGLYFLASMF FTPLVTNVPR WAVGPSLVMV GVMMMGVVKD IRWGETKEAV TAFVTILLMP LTYSI ANGI IAGIGIYLAL SMYDVVLGVA KWLNGVRKRV MREHNQVSSV ATVEIV

UniProtKB: Adenine/guanine permease AZG2

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65805
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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