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- EMDB-35679: Endogenous substrate adenine bound state of Arabidopsis AZG1 at pH 5.5 -

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Basic information

Entry
Database: EMDB / ID: EMD-35679
TitleEndogenous substrate adenine bound state of Arabidopsis AZG1 at pH 5.5
Map data
Sample
  • Complex: complex of AZG1 and Adenine
    • Protein or peptide: Adenine/guanine permease AZG1
  • Ligand: ADENINE
  • Ligand: water
Keywordscytokinin / transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


adenine transport / guanine transport / purine nucleobase transmembrane transporter activity / purine nucleobase 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: 2.6 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
DepositionMar 19, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35679.png

Downloads & links

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Map

FileDownload / File: emd_35679.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.851 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.05740285 - 0.118583865
Average (Standard dev.)-0.000032008724 (±0.0038098583)
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_35679_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_35679_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : complex of AZG1 and Adenine

EntireName: complex of AZG1 and Adenine
Components
  • Complex: complex of AZG1 and Adenine
    • Protein or peptide: Adenine/guanine permease AZG1
  • Ligand: ADENINE
  • Ligand: water

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Supramolecule #1: complex of AZG1 and Adenine

SupramoleculeName: complex of AZG1 and Adenine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 65.686703 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 TSPVTVFIES 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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Macromolecule #3: ADENINE

MacromoleculeName: ADENINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADE
Molecular weightTheoretical: 135.127 Da
Chemical component information

ChemComp-ADE:
ADENINE / Adenine

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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: 5.5
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 235460

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