[English] 日本語
Yorodumi
- EMDB-14117: Inward-facing NPA bound form of auxin transporter PIN8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14117
TitleInward-facing NPA bound form of auxin transporter PIN8
Map data
Sample
  • Complex: NPA-form of PIN8
    • Protein or peptide: Auxin efflux carrier component 8
  • Ligand: 2-(naphthalen-1-ylcarbamoyl)benzoic acid
  • Ligand: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water
KeywordsAuxin transport / AEC family / BART superfamily / MEMBRANE PROTEIN
Function / homology
Function and homology information


auxin export across the plasma membrane / auxin efflux transmembrane transporter activity / pollen development / auxin-activated signaling pathway / cell periphery / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Auxin efflux carrier, plant type / : / Membrane transport protein / Membrane transport protein
Similarity search - Domain/homology
Auxin efflux carrier component 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsUng KL / Winkler MBL
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101000936European Union
CitationJournal: Nature / Year: 2022
Title: Structures and mechanism of the plant PIN-FORMED auxin transporter.
Authors: Kien Lam Ung / Mikael Winkler / Lukas Schulz / Martina Kolb / Dorina P Janacek / Emil Dedic / David L Stokes / Ulrich Z Hammes / Bjørn Panyella Pedersen /
Abstract: Auxins are hormones that have central roles and control nearly all aspects of growth and development in plants. The proteins in the PIN-FORMED (PIN) family (also known as the auxin efflux carrier ...Auxins are hormones that have central roles and control nearly all aspects of growth and development in plants. The proteins in the PIN-FORMED (PIN) family (also known as the auxin efflux carrier family) are key participants in this process and control auxin export from the cytosol to the extracellular space. Owing to a lack of structural and biochemical data, the molecular mechanism of PIN-mediated auxin transport is not understood. Here we present biophysical analysis together with three structures of Arabidopsis thaliana PIN8: two outward-facing conformations with and without auxin, and one inward-facing conformation bound to the herbicide naphthylphthalamic acid. The structure forms a homodimer, with each monomer divided into a transport and scaffold domain with a clearly defined auxin binding site. Next to the binding site, a proline-proline crossover is a pivot point for structural changes associated with transport, which we show to be independent of proton and ion gradients and probably driven by the negative charge of the auxin. The structures and biochemical data reveal an elevator-type transport mechanism reminiscent of bile acid/sodium symporters, bicarbonate/sodium symporters and sodium/proton antiporters. Our results provide a comprehensive molecular model for auxin recognition and transport by PINs, link and expand on a well-known conceptual framework for transport, and explain a central mechanism of polar auxin transport, a core feature of plant physiology, growth and development.
History
DepositionJan 3, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14117.png

Downloads & links

-
Map

FileDownload / File: emd_14117.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 208 pix.
= 269.152 Å		1.29 Å/pix.
x 208 pix.
= 269.152 Å		1.29 Å/pix.
x 208 pix.
= 269.152 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.294 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-1.3408047 - 1.8188517
Average (Standard dev.)0.00046474155 (±0.039535314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 269.152 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_14117_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_14117_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_14117_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : NPA-form of PIN8

EntireName: NPA-form of PIN8
Components
  • Complex: NPA-form of PIN8
    • Protein or peptide: Auxin efflux carrier component 8
  • Ligand: 2-(naphthalen-1-ylcarbamoyl)benzoic acid
  • Ligand: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water

-
Supramolecule #1: NPA-form of PIN8

SupramoleculeName: NPA-form of PIN8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: dimer form of PIN8
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 81 KDa

-
Macromolecule #1: Auxin efflux carrier component 8

MacromoleculeName: Auxin efflux carrier component 8 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 41.541039 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGISWLDIYH VVSATVPLYV SMTLGFLSAR HLKLFSPEQC AGINKFVAKF SIPLLSFQII SENNPFKMSP KLILSDILQK FLVVVVLAM VLRFWHPTGG RGGKLGWVIT GLSISVLPNT LILGMPILSA IYGDEAASIL EQIVVLQSLI WYTILLFLFE L NAARALPS ...String:
MGISWLDIYH VVSATVPLYV SMTLGFLSAR HLKLFSPEQC AGINKFVAKF SIPLLSFQII SENNPFKMSP KLILSDILQK FLVVVVLAM VLRFWHPTGG RGGKLGWVIT GLSISVLPNT LILGMPILSA IYGDEAASIL EQIVVLQSLI WYTILLFLFE L NAARALPS SGASLEHTGN DQEEANIEDE PKEEEDEEEV AIVRTRSVGT MKILLKAWRK LIINPNTYAT LIGIIWATLH FR LGWNLPE MIDKSIHLLS DGGLGMAMFS LGLFMASQSS IIACGTKMAI ITMLLKFVLG PALMIASAYC IRLKSTLFKV AIL QAALPQ GVVPFVFAKE YNLHPEIIST GVIFGMLIAL PTTLAYYFLL DLPGENLYFQ

UniProtKB: Auxin efflux carrier component 8

-
Macromolecule #2: 2-(naphthalen-1-ylcarbamoyl)benzoic acid

MacromoleculeName: 2-(naphthalen-1-ylcarbamoyl)benzoic acid / type: ligand / ID: 2 / Number of copies: 2 / Formula: E7O
Molecular weightTheoretical: 291.301 Da
Chemical component information

ChemComp-E7O:
2-(naphthalen-1-ylcarbamoyl)benzoic acid

-
Macromolecule #3: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: DLP
Molecular weightTheoretical: 782.082 Da
Chemical component information

ChemComp-DLP:
1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 62 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
150.0 mMNaClsodium chloride
0.5 mMC10H16N2O8EDTA
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: The grid was glow-discharge at 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Wait 4 seconds after sample loading, Blotting time 4 seconds with blotting force of -1 before plunging.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 14500 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3345146
Startup modelType of model: INSILICO MODEL / In silico model: RoseTTAfold model (Baek et al.,2021) / Details: Sequence used: UniProt Q9LFP6
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: Non-uniform refinement job / Number images used: 77608
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: ab initio job / Details: Cryosparc ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: non-uniform refinement job / Details: Cryosparc NU refinement
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: Heterogenous Refinement Job
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