[English] 日本語
Yorodumi
- EMDB-35678: Apo state of Arabidopsis AZG1 at pH 7.4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35678
TitleApo state of Arabidopsis AZG1 at pH 7.4
Map data
Sample
  • Complex: AZG1 dimer
    • Protein or peptide: Adenine/guanine permease AZG1
Keywordscytokinin / transporter / TRANSPORT 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: 2.7 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

-
Structure visualization

Supplemental images

emd_35678.png

Downloads & links

-
Map

FileDownload / File: emd_35678.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.851 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.058253847 - 0.10506887
Average (Standard dev.)-0.000008315473 (±0.0038716989)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #1

Fileemd_35678_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_35678_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : AZG1 dimer

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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 5.5
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 292160
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more