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- EMDB-37681: Apo state of Arabidopsis AZG1 T440Y -

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Basic information

Entry
Database: EMDB / ID: EMD-37681
TitleApo state of Arabidopsis AZG1 T440Y
Map data
Sample
  • Complex: AZG1 dimer
    • Protein or peptide: Adenine/guanine permease AZG1
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


guanine transport / purine nucleobase transmembrane transporter activity / purine nucleobase transport / adenine transport / membrane / cytosol
Similarity search - Function
Azaguanine-like transporters / Nucleobase cation symporter 2 family / Permease family
Similarity search - Domain/homology
Adenine/guanine permease AZG1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsXu L / Guo J
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303400 China
Ministry of Science and Technology (MoST, China)2020YFA0908501 China
Ministry of Science and Technology (MoST, China)2020YFA0908400 China
CitationJournal: Nat Plants / Year: 2024
Title: Structures and mechanisms of the Arabidopsis cytokinin transporter AZG1.
Authors: Lingyi Xu / Wei Jia / Xin Tao / Fan Ye / Yan Zhang / Zhong Jie Ding / Shao Jian Zheng / Shuai Qiao / Nannan Su / Yu Zhang / Shan Wu / Jiangtao Guo /
Abstract: Cytokinins are essential for plant growth and development, and their tissue distributions are regulated by transmembrane transport. Recent studies have revealed that members of the 'Aza-Guanine ...Cytokinins are essential for plant growth and development, and their tissue distributions are regulated by transmembrane transport. Recent studies have revealed that members of the 'Aza-Guanine Resistant' (AZG) protein family from Arabidopsis thaliana can mediate cytokinin uptake in roots. Here we present 2.7 to 3.3 Å cryo-electron microscopy structures of Arabidopsis AZG1 in the apo state and in complex with its substrates trans-zeatin (tZ), 6-benzyleaminopurine (6-BAP) or kinetin. AZG1 forms a homodimer and each subunit shares a similar topology and domain arrangement with the proteins of the nucleobase/ascorbate transporter (NAT) family. These structures, along with functional analyses, reveal the molecular basis for cytokinin recognition. Comparison of the AZG1 structures determined in inward-facing conformations and predicted by AlphaFold2 in the occluded conformation allowed us to propose that AZG1 may carry cytokinins across the membrane through an elevator mechanism.
History
DepositionOct 6, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37681.png

Downloads & links

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Map

FileDownload / File: emd_37681.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 240 pix.
= 204.24 Å		0.85 Å/pix.
x 240 pix.
= 204.24 Å		0.85 Å/pix.
x 240 pix.
= 204.24 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.851 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.049857054 - 0.08334622
Average (Standard dev.)-0.00010038008 (±0.0028296874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 204.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37681_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37681_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AZG1 dimer

EntireName: AZG1 dimer
Components
  • Complex: AZG1 dimer
    • Protein or peptide: Adenine/guanine permease AZG1

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Supramolecule #1: AZG1 dimer

SupramoleculeName: AZG1 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 131.2 KDa

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Macromolecule #1: Adenine/guanine permease AZG1

MacromoleculeName: Adenine/guanine permease AZG1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 65.748773 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEQQQQQQLP STTTRPKPKL LNRLNTYVGS SRVGKRFKLA ERNSTFTTEL RAGTATFLTM AYILAVNASI LSDSGGTCSV SDCIPLCSN PAIEPSQCTG PGLRLIQPDV SCKFNPVNPG YAACVEEIRK DLIVATVAAS LIGCVIMGLM ANLPLALAPG M GTNAYFAY ...String:
MEQQQQQQLP STTTRPKPKL LNRLNTYVGS SRVGKRFKLA ERNSTFTTEL RAGTATFLTM AYILAVNASI LSDSGGTCSV SDCIPLCSN PAIEPSQCTG PGLRLIQPDV SCKFNPVNPG YAACVEEIRK DLIVATVAAS LIGCVIMGLM ANLPLALAPG M GTNAYFAY TVVGFHGSGS ISYRTALAAV FIEGLIFLFI SAIGFRAKLA KLVPKPVRIS SSAGIGLFLA FIGLQNNQGI GL VGYSPST LVTLAACPAS SRISLAPVIT SANGTVSLLA GGSVSGDIMC IHGRMESPTF WLGIVGFVII AYCLVKNVKG AMI YGIVFV TAVSWFRNTE VTAFPNTSAG DAAHDYFKKI VDVHVIKHTA GALSFSGINK GHFWEALVTF LYVDILDTTG TLYS MARFA GFVDEKGDFA GQYFAFMSDA SAIVIGSLLG TSPVYVFIES STGIREGGRT GLTAITVAVY FLLAMFFTPL LASIP AWAV GPPLILVGVM MMKSVTEIDW EDMREAIPAF VTMILMPLTY SVAYGLIGGI GSYVVLHLWD WGEEGLVKLG FLKRKV KEE DNNNGVVKAS EIDTTVSGRD YKDDDDKWSH PQFEKGGGGS GGSAWSHPQF EK

UniProtKB: Adenine/guanine permease AZG1

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1097561
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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