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- EMDB-61071: Structure of the wild-type AZG2 in Arabidopsis thaliana in the tr... -

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Basic information

Entry
Database: EMDB / ID: EMD-61071
TitleStructure of the wild-type AZG2 in Arabidopsis thaliana in the trans-Zeatin-bound state-2 at pH 7.4
Map data
Sample
  • Complex: AZG2 dimer
    • Protein or peptide: Adenine/guanine permease AZG2
  • Ligand: (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol
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: 3.5 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: To Be Published
Title: Structure of the wild-type AZG2 in Arabidopsis thaliana in the trans-Zeatin-bound state-2 at pH 7.4
Authors: Sun L / Liu X / Wei H / Yang Z / Ying W
History
DepositionAug 3, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61071.png

Downloads & links

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Map

FileDownload / File: emd_61071.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.)
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.2446355 - 1.8882042
Average (Standard dev.)0.0013406364 (±0.045518618)
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_61071_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61071_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_61071_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 : AZG2 dimer

EntireName: AZG2 dimer
Components
  • Complex: AZG2 dimer
    • Protein or peptide: Adenine/guanine permease AZG2
  • Ligand: (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol

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Supramolecule #1: AZG2 dimer

SupramoleculeName: AZG2 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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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Macromolecule #2: (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol

MacromoleculeName: (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZEA
Molecular weightTheoretical: 219.243 Da
Chemical component information

ChemComp-ZEA:
(2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol

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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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49865
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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