[English] 日本語
Yorodumi
- EMDB-37836: Cryo-EM structure of jasmonic acid transporter ABCG16 bound to JA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37836
TitleCryo-EM structure of jasmonic acid transporter ABCG16 bound to JA
Map data
Sample
  • Complex: Homodimer of ABCG16
    • Protein or peptide: ABC transporter G family member 16
  • Ligand: {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid
Keywordsjasmonate / transport / cryo-EM / ABC transporter / plant hormone / MEMBRANE PROTEIN
Function / homology
Function and homology information


pollen wall assembly / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
: / ABC-2 type transporter / ABC-2 type transporter / ABC transporter-like, conserved site / ABC transporters family signature. / 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 16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsHuang X / An N / Zhang X / Zhang P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Plants / Year: 2024
Title: Cryo-EM structure and molecular mechanism of the jasmonic acid transporter ABCG16.
Authors: Ning An / Xiaowei Huang / Zhao Yang / Minhua Zhang / Miaolian Ma / Fang Yu / Lianyan Jing / Boya Du / Yong-Fei Wang / Xue Zhang / Peng Zhang /
Abstract: Jasmonates (JAs) are a class of oxylipin phytohormones including jasmonic acid (JA) and derivatives that regulate plant growth, development and biotic and abiotic stress. A number of transporters ...Jasmonates (JAs) are a class of oxylipin phytohormones including jasmonic acid (JA) and derivatives that regulate plant growth, development and biotic and abiotic stress. A number of transporters have been identified to be responsible for the cellular and subcellular translocation of JAs. However, the mechanistic understanding of how these transporters specifically recognize and transport JAs is scarce. Here we determined the cryogenic electron microscopy structure of JA exporter AtABCG16 in inward-facing apo, JA-bound and occluded conformations, and outward-facing post translocation conformation. AtABCG16 structure forms a homodimer, and each monomer contains a nucleotide-binding domain, a transmembrane domain and an extracellular domain. Structural analyses together with biochemical and plant physiological experiments revealed the molecular mechanism by which AtABCG16 specifically recognizes and transports JA. Structural analyses also revealed that AtABCG16 features a unique bifurcated substrate translocation pathway, which is composed of two independent substrate entrances, two substrate-binding pockets and a shared apoplastic cavity. In addition, residue Phe608 from each monomer is disclosed to function as a gate along the translocation pathway controlling the accessing of substrate JA from the cytoplasm or apoplast. Based on the structural and biochemical analyses, a working model of AtABCG16-mediated JA transport is proposed, which diversifies the molecular mechanisms of ABC transporters.
History
DepositionOct 19, 2023-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37836.png

Downloads & links

-
Map

FileDownload / File: emd_37836.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.4128084 - 4.6969323
Average (Standard dev.)-0.00065655605 (±0.11105891)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: unsharpened map

Fileemd_37836_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_37836_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37836_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homodimer of ABCG16

EntireName: Homodimer of ABCG16
Components
  • Complex: Homodimer of ABCG16
    • Protein or peptide: ABC transporter G family member 16
  • Ligand: {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid

-
Supramolecule #1: Homodimer of ABCG16

SupramoleculeName: Homodimer of ABCG16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
Macromolecule #1: ABC transporter G family member 16

MacromoleculeName: ABC transporter G family member 16 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 81.79243 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSRILVEDDN ATPFHSMEII SSSLTLGQLL KNVSDVRKVE VGDETPVHEF FDRDGSSLDG DNDHLMRPVP FVLSFNNLTY NVSVRRKLD FHDLVPWRRT SFSKTKTLLD NISGETRDGE ILAVLGASGS GKSTLIDALA NRIAKGSLKG TVTLNGEALQ S RMLKVISA ...String:
MSRILVEDDN ATPFHSMEII SSSLTLGQLL KNVSDVRKVE VGDETPVHEF FDRDGSSLDG DNDHLMRPVP FVLSFNNLTY NVSVRRKLD FHDLVPWRRT SFSKTKTLLD NISGETRDGE ILAVLGASGS GKSTLIDALA NRIAKGSLKG TVTLNGEALQ S RMLKVISA YVMQDDLLFP MLTVEETLMF AAEFRLPRSL PKSKKKLRVQ ALIDQLGIRN AAKTIIGDEG HRGISGGERR RV SIGIDII HDPIVLFLDE PTSGLDSTSA FMVVKVLKRI AESGSIIIMS IHQPSHRVLS LLDRLIFLSR GHTVFSGSPA SLP SFFAGF GNPIPENENQ TEFALDLIRE LEGSAGGTRG LVEFNKKWQE MKKQSNPQTL TPPASPNPNL TLKEAISASI SRGK LVSGG GGGSSVINHG GGTLAVPAFA NPFWIEIKTL TRRSILNSRR QPELLGMRLA TVIVTGFILA TVFWRLDNSP KGVQE RLGF FAFAMSTMFY TCADALPVFL QERYIFMRET AYNAYRRSSY VLSHAIVTFP SLIFLSLAFA VTTFWAVGLE GGLMGF LFY CLIILASFWS GSSFVTFLSG VVPHVMLGYT IVVAILAYFL LFSGFFINRD RIPQYWIWFH YLSLVKYPYE AVLQNEF SD PTECFVRGVQ LFDNSPLGEL TYGMKLRLLD SVSRSIGMRI SSSTCLTTGA DVLKQQGVTQ LSKWNCLLIT VGFGFLFR I LFYLCLLLGS KNKRR

UniProtKB: ABC transporter G family member 16

-
Macromolecule #2: {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid

MacromoleculeName: {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid
type: ligand / ID: 2 / Number of copies: 2 / Formula: JAA
Molecular weightTheoretical: 210.27 Da
Chemical component information

ChemComp-JAA:
{(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid / hormone*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 607125
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