[English] 日本語
Yorodumi
- EMDB-37397: Cryo-EM structure of the ABCG25 E232Q mutant bound to ATP and Mag... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37397
TitleCryo-EM structure of the ABCG25 E232Q mutant bound to ATP and Magnesium
Map data
Sample
  • Complex: Homodimer of ABCG25 E211Q mutant bound to ATP and Magnesium
    • Protein or peptide: ABC transporter G family member 25
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsexporter / complex / transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


intercellular transport / negative regulation of post-embryonic development / abscisic acid transport / export from cell / response to abscisic acid / abscisic acid-activated signaling pathway / efflux transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / response to cold ...intercellular transport / negative regulation of post-embryonic development / abscisic acid transport / export from cell / response to abscisic acid / abscisic acid-activated signaling pathway / efflux transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / response to cold / transmembrane transport / response to heat / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter family G domain / ABC-2 type transporter / : / ABC-2 type transporter / ABC-2 type transporter / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter G family member 25
Similarity search - Component
Biological speciesArabidopsis arenosa (plant) / Arabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsXin J / Yan KG
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271251 China
Citation
Journal: Plant Commun / Year: 2024
Title: Structural insights into AtABCG25, an angiosperm-specific abscisic acid exporter.
Authors: Jian Xin / Yeling Zhou / Yichun Qiu / He Geng / Yuzhu Wang / Yi Song / Jiansheng Liang / Kaige Yan /
Abstract: Cellular hormone homeostasis is essential for precise spatial and temporal signaling responses and plant fitness. Abscisic acid (ABA) plays pivotal roles in orchestrating various developmental and ...Cellular hormone homeostasis is essential for precise spatial and temporal signaling responses and plant fitness. Abscisic acid (ABA) plays pivotal roles in orchestrating various developmental and stress responses and confers fitness benefits over ecological and evolutionary timescales in terrestrial plants. Cellular ABA level is regulated by complex processes, including biosynthesis, catabolism, and transport. AtABCG25 is the first ABA exporter identified through genetic screening and affects diverse ABA responses. Resolving the structural basis of ABA export by ABCG25 is critical for further manipulations of ABA homeostasis and plant fitness. We used cryo-electron microscopy to elucidate the structural dynamics of AtABCG25 and successfully characterized different states, including apo AtABCG25, ABA-bound AtABCG25, and ATP-bound AtABCG25 (E232Q). Notably, AtABCG25 forms a homodimer that features a deep, slit-like cavity in the transmembrane domain, and we precisely characterized the critical residues in the cavity where ABA binds. ATP binding triggers closure of the nucleotide-binding domains and conformational transitions in the transmembrane domains. We show that AtABCG25 belongs to a conserved ABCG subfamily that originated during the evolution of angiosperms. This subfamily neofunctionalized to regulate seed germination via the endosperm, in concert with the evolution of this angiosperm-specific, embryo-nourishing tissue. Collectively, these findings provide valuable insights into the intricate substrate recognition and transport mechanisms of the ABA exporter AtABCG25, paving the way for genetic manipulation of ABA homeostasis and plant fitness.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Xin J / Yan KG
History
DepositionSep 7, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37397.png

Downloads & links

-
Map

FileDownload / File: emd_37397.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 280.32 Å		1.1 Å/pix.
x 256 pix.
= 280.32 Å		1.1 Å/pix.
x 256 pix.
= 280.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-2.1122808 - 3.5302515
Average (Standard dev.)-0.0022072103 (±0.07068637)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 280.32 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_37397_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37397_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homodimer of ABCG25 E211Q mutant bound to ATP and Magnesium

EntireName: Homodimer of ABCG25 E211Q mutant bound to ATP and Magnesium
Components
  • Complex: Homodimer of ABCG25 E211Q mutant bound to ATP and Magnesium
    • Protein or peptide: ABC transporter G family member 25
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Homodimer of ABCG25 E211Q mutant bound to ATP and Magnesium

SupramoleculeName: Homodimer of ABCG25 E211Q mutant bound to ATP and Magnesium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis arenosa (plant)

-
Macromolecule #1: ABC transporter G family member 25

MacromoleculeName: ABC transporter G family member 25 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 77.120164 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDHDGDY KDHDIDYKDD DDKGSDLEVL FQGPGSMSAF DGVENQMNGP DSSPRLSQDP REPRSLLSSS CFPITLKFVD VCYRVKIHG MSNDSCNIKK LLGLKQKPSD ETRSTEERTI LSGVTGMISP GEFMAVLGPS GSGKSTLLNA VAGRLHGSNL T GKILINDG ...String:
MDYKDHDGDY KDHDIDYKDD DDKGSDLEVL FQGPGSMSAF DGVENQMNGP DSSPRLSQDP REPRSLLSSS CFPITLKFVD VCYRVKIHG MSNDSCNIKK LLGLKQKPSD ETRSTEERTI LSGVTGMISP GEFMAVLGPS GSGKSTLLNA VAGRLHGSNL T GKILINDG KITKQTLKRT GFVAQDDLLY PHLTVRETLV FVALLRLPRS LTRDVKLRAA ESVISELGLT KCENTVVGNT FI RGISGGE RKRVSIAHEL LINPSLLVLD QPTSGLDATA ALRLVQTLAG LAHGKGKTVV TSIHQPSSRV FQMFDTVLLL SEG KCLFVG KGRDAMAYFE SVGFSPAFPM NPADFLLDLA NGVCQTDGVT EREKPNVRQT LVTAYDTLLA PQVKTCIEVS HFPQ DNARF VKTRVNGGGI TTCIATWFSQ LCILLHRLLK ERRHESFDLL RIFQVVAASI LCGLMWWHSD YRDVHDRLGL LFFIS IFWG VLPSFNAVFT FPQERAIFTR ERASGMYTLS SYFMAHVLGS LSMELVLPAS FLTFTYWMVY LRPGIVPFLL TLSVLL LYV LASQGLGLAL GAAIMDAKKA STIVTVTMLA FVLTGGYYVN KVPSGMVWMK YVSTTFYCYR LLVAIQYGSG EEILRML GC DSKGKQGASA ATSAGCRFVE EEVIGDVGMW TSVGVLFLMF FGYRVLAYLA LRRIKH

UniProtKB: ABC transporter G family member 25

-
Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6.8 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88408
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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