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- EMDB-33500: IAA bound state of AtPIN3 -

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Basic information

Entry
Database: EMDB / ID: EMD-33500
TitleIAA bound state of AtPIN3
Map dataIAA bound state of AtPIN3
Sample
  • Complex: IAA-bound state AtPIN3(AtPIN3-IAA)
    • Protein or peptide: Auxin efflux carrier component 3
  • Ligand: 1H-INDOL-3-YLACETIC ACID
KeywordsPIN-FORMED (PIN) protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


tropism / root hair initiation / root hair elongation / positive gravitropism / gravitropism / auxin export across the plasma membrane / auxin polar transport / auxin efflux transmembrane transporter activity / root development / auxin-activated signaling pathway ...tropism / root hair initiation / root hair elongation / positive gravitropism / gravitropism / auxin export across the plasma membrane / auxin polar transport / auxin efflux transmembrane transporter activity / root development / auxin-activated signaling pathway / vesicle membrane / response to light stimulus / lateral plasma membrane / cell surface / protein homodimerization activity / mitochondrion / 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 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsSu N
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0908501 China
Ministry of Science and Technology (MoST, China)2018YFA0508100 China
CitationJournal: Nature / Year: 2022
Title: Structures and mechanisms of the Arabidopsis auxin transporter PIN3.
Authors: Nannan Su / Aiqin Zhu / Xin Tao / Zhong Jie Ding / Shenghai Chang / Fan Ye / Yan Zhang / Cheng Zhao / Qian Chen / Jiangqin Wang / Chen Yu Zhou / Yirong Guo / Shasha Jiao / Sufen Zhang / Han ...Authors: Nannan Su / Aiqin Zhu / Xin Tao / Zhong Jie Ding / Shenghai Chang / Fan Ye / Yan Zhang / Cheng Zhao / Qian Chen / Jiangqin Wang / Chen Yu Zhou / Yirong Guo / Shasha Jiao / Sufen Zhang / Han Wen / Lixin Ma / Sheng Ye / Shao Jian Zheng / Fan Yang / Shan Wu / Jiangtao Guo /
Abstract: The PIN-FORMED (PIN) protein family of auxin transporters mediates polar auxin transport and has crucial roles in plant growth and development. Here we present cryo-electron microscopy structures of ...The PIN-FORMED (PIN) protein family of auxin transporters mediates polar auxin transport and has crucial roles in plant growth and development. Here we present cryo-electron microscopy structures of PIN3 from Arabidopsis thaliana in the apo state and in complex with its substrate indole-3-acetic acid and the inhibitor N-1-naphthylphthalamic acid (NPA). A. thaliana PIN3 exists as a homodimer, and its transmembrane helices 1, 2 and 7 in the scaffold domain are involved in dimerization. The dimeric PIN3 forms a large, joint extracellular-facing cavity at the dimer interface while each subunit adopts an inward-facing conformation. The structural and functional analyses, along with computational studies, reveal the structural basis for the recognition of indole-3-acetic acid and NPA and elucidate the molecular mechanism of NPA inhibition on PIN-mediated auxin transport. The PIN3 structures support an elevator-like model for the transport of auxin, whereby the transport domains undergo up-down rigid-body motions and the dimerized scaffold domains remain static.
History
DepositionMay 29, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33500.png

Downloads & links

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Map

FileDownload / File: emd_33500.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIAA bound state of AtPIN3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 240 pix.
= 223.2 Å		0.93 Å/pix.
x 240 pix.
= 223.2 Å		0.93 Å/pix.
x 240 pix.
= 223.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0168
Minimum - Maximum-0.072674885 - 0.120523
Average (Standard dev.)-0.000006221864 (±0.003155269)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 223.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33500_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1 map of AtPIN3 IAA

Fileemd_33500_half_map_1.map
Annotationhalf1 map of AtPIN3_IAA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2 map of AtPIN3 IAA

Fileemd_33500_half_map_2.map
Annotationhalf2 map of AtPIN3_IAA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : IAA-bound state AtPIN3(AtPIN3-IAA)

EntireName: IAA-bound state AtPIN3(AtPIN3-IAA)
Components
  • Complex: IAA-bound state AtPIN3(AtPIN3-IAA)
    • Protein or peptide: Auxin efflux carrier component 3
  • Ligand: 1H-INDOL-3-YLACETIC ACID

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Supramolecule #1: IAA-bound state AtPIN3(AtPIN3-IAA)

SupramoleculeName: IAA-bound state AtPIN3(AtPIN3-IAA) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Auxin efflux carrier component 3

MacromoleculeName: Auxin efflux carrier component 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 73.983531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKWS HPQFEKGGGG SGGSAWSHPQ FEKEFKGLVD MISWHDLYTV LTAVIPLYVA MILAYGSVRW WKIFSPDQCS GINRFVAIF AVPLLSFHFI STNNPYAMNL RFIAADTLQK IIMLSLLVLW ANFTRSGSLE WSITIFSLST LPNTLVMGIP L LIAMYGEY ...String:
DYKDDDDKWS HPQFEKGGGG SGGSAWSHPQ FEKEFKGLVD MISWHDLYTV LTAVIPLYVA MILAYGSVRW WKIFSPDQCS GINRFVAIF AVPLLSFHFI STNNPYAMNL RFIAADTLQK IIMLSLLVLW ANFTRSGSLE WSITIFSLST LPNTLVMGIP L LIAMYGEY SGSLMVQIVV LQCIIWYTLL LFLFEFRGAK MLIMEQFPET AASIVSFKVE SDVVSLDGHD FLETDAEIGD DG KLHVTVR KSNASRRSFC GPNMTPRPSN LTGAEIYSLS TTPRGSNFNH SDFYNMMGFP GGRLSNFGPA DMYSVQSSRG PTP RPSNFE ENCAMASSPR FGYYPGGGAG SYPAPNPEFS STTTSTANKS VNKNPKDVNT NQQTTLPTGG KSNSHDAKEL HMFV WSSNG SPVSDRAGLN VFGGAPDNDQ GGRSDQGAKE IRMLVPDQSH NGETKAVAHP ASGDFGGEQQ FSFAGKEEEA ERPKD AENG LNKLAPNSTA ALQSKTGLGG AEASQRKNMP PASVMTRLIL IMVWRKLIRN PNTYSSLIGL IWALVAFRWH VAMPKI IQQ SISILSDAGL GMAMFSLGLF MALQPKLIAC GNSVATFAMA VRFLTGPAVM AVAAIAIGLR GDLLRVAIVQ AALPQGI VP FVFAKEYNVH PAILSTGVIF GMLIALPITL VYYILLGL

UniProtKB: Auxin efflux carrier component 3

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Macromolecule #2: 1H-INDOL-3-YLACETIC ACID

MacromoleculeName: 1H-INDOL-3-YLACETIC ACID / type: ligand / ID: 2 / Number of copies: 2 / Formula: IAC
Molecular weightTheoretical: 175.184 Da
Chemical component information

ChemComp-IAC:
1H-INDOL-3-YLACETIC ACID / hormone*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 6.0 sec. / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 177699
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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