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- PDB-9j13: Structure of the wild-type AZG2 in Arabidopsis thaliana in the ap... -

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Basic information

Entry
Database: PDB / ID: 9j13
TitleStructure of the wild-type AZG2 in Arabidopsis thaliana in the apo state at pH 7.4
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: 3.4 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: To Be Published
Title: Structure of the wild-type AZG2 in Arabidopsis thaliana in the apo state at pH 7.4
Authors: Sun, L. / Liu, X. / Wei, H. / Yang, Z. / Ying, W.
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
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Primary map / Data content type: Primary map / 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: 7.4
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65805 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023795
ELECTRON MICROSCOPYf_angle_d0.5245159
ELECTRON MICROSCOPYf_dihedral_angle_d4.359531
ELECTRON MICROSCOPYf_chiral_restr0.04626
ELECTRON MICROSCOPYf_plane_restr0.004635

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