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- EMDB-33692: Structure of the auxin exporter PIN1 in Arabidopsis thaliana in t... -

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Basic information

Entry
Database: EMDB / ID: EMD-33692
TitleStructure of the auxin exporter PIN1 in Arabidopsis thaliana in the NPA-bound state
Map dataEM map
Sample
  • Complex: AtPIN1 in complex with a nanobody and NPA
    • Complex: AtPIN1
      • Protein or peptide: Auxin efflux carrier component 1
    • Complex: nanobody
      • Protein or peptide: nanobody
  • Ligand: 2-(naphthalen-1-ylcarbamoyl)benzoic acid
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


cotyledon morphogenesis / leaf formation / cotyledon development / leaf shaping / shoot system development / xylem and phloem pattern formation / inflorescence development / gravitropism / auxin export across the plasma membrane / auxin efflux transmembrane transporter activity ...cotyledon morphogenesis / leaf formation / cotyledon development / leaf shaping / shoot system development / xylem and phloem pattern formation / inflorescence development / gravitropism / auxin export across the plasma membrane / auxin efflux transmembrane transporter activity / flower development / auxin polar transport / root development / plant-type cell wall / photomorphogenesis / embryo development ending in seed dormancy / auxin-activated signaling pathway / plasmodesma / basal plasma membrane / cell periphery / apical part of cell / apical plasma membrane / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Auxin efflux carrier, plant type / : / Membrane transport protein / Membrane transport protein
Similarity search - Domain/homology
Auxin efflux carrier component 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSun L / Liu X / Yang Z / Xia J
Funding support China, 4 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37020103 China
National Natural Science Foundation of China (NSFC)31900885 and 31870732 China
Other government2008085MC90 and 2008085J15 China
Other governmentWK9100000031 and YD9100002004 China
CitationJournal: Nature / Year: 2022
Title: Structural insights into auxin recognition and efflux by Arabidopsis PIN1.
Authors: Zhisen Yang / Jing Xia / Jingjing Hong / Chenxi Zhang / Hong Wei / Wei Ying / Chunqiao Sun / Lianghanxiao Sun / Yanbo Mao / Yongxiang Gao / Shutang Tan / Jiří Friml / Dianfan Li / Xin Liu / Linfeng Sun /
Abstract: Polar auxin transport is unique to plants and coordinates their growth and development. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and ...Polar auxin transport is unique to plants and coordinates their growth and development. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and drive polar auxin transport; however, their structures and transport mechanisms remain largely unknown. Here, we report three inward-facing conformation structures of Arabidopsis thaliana PIN1: the apo state, bound to the natural auxin indole-3-acetic acid (IAA), and in complex with the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). The transmembrane domain of PIN1 shares a conserved NhaA fold. In the substrate-bound structure, IAA is coordinated by both hydrophobic stacking and hydrogen bonding. NPA competes with IAA for the same site at the intracellular pocket, but with a much higher affinity. These findings inform our understanding of the substrate recognition and transport mechanisms of PINs and set up a framework for future research on directional auxin transport, one of the most crucial processes underlying plant development.
History
DepositionJun 26, 2022-
Header (metadata) releaseSep 7, 2022-
Map releaseSep 7, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33692.png

Downloads & links

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Map

FileDownload / File: emd_33692.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.5682933 - 5.746463
Average (Standard dev.)0.0035168338 (±0.11568965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_33692_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_33692_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AtPIN1 in complex with a nanobody and NPA

EntireName: AtPIN1 in complex with a nanobody and NPA
Components
  • Complex: AtPIN1 in complex with a nanobody and NPA
    • Complex: AtPIN1
      • Protein or peptide: Auxin efflux carrier component 1
    • Complex: nanobody
      • Protein or peptide: nanobody
  • Ligand: 2-(naphthalen-1-ylcarbamoyl)benzoic acid

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Supramolecule #1: AtPIN1 in complex with a nanobody and NPA

SupramoleculeName: AtPIN1 in complex with a nanobody and NPA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Supramolecule #2: AtPIN1

SupramoleculeName: AtPIN1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: nanobody

SupramoleculeName: nanobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: Auxin efflux carrier component 1

MacromoleculeName: Auxin efflux carrier component 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 67.080781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MITAADFYHV MTAMVPLYVA MILAYGSVKW WKIFTPDQCS GINRFVALFA VPLLSFHFIA ANNPYAMNLR FLAADSLQKV IVLSLLFLW CKLSRNGSLD WTITLFSLST LPNTLVMGIP LLKGMYGNFS GDLMVQIVVL QCIIWYTLML FLFEYRGAKL L ISEQFPDT ...String:
MITAADFYHV MTAMVPLYVA MILAYGSVKW WKIFTPDQCS GINRFVALFA VPLLSFHFIA ANNPYAMNLR FLAADSLQKV IVLSLLFLW CKLSRNGSLD WTITLFSLST LPNTLVMGIP LLKGMYGNFS GDLMVQIVVL QCIIWYTLML FLFEYRGAKL L ISEQFPDT AGSIVSIHVD SDIMSLDGRQ PLETEAEIKE DGKLHVTVRR SNASRSDIYS RRSQGLSATP RPSNLTNAEI YS LQSSRNP TPRGSSFNHT DFYSMMASGG GRNSNFGPGE AVFGSKGPTP RPSNYEEDGG PAKPTAAGTA AGAGRFHYQS GGS GGGGGA HYPAPNPGMF SPNTGGGGGT AAKGNAPVVG GKRQDGNGRD LHMFVWSSSA SPVSDVFGGG GGNHHADYST ATND HQKDV KISVPQGNSN DNQYVEREEF SFGNKDDDSK VLATDGGNNI SNKTTQAKVM PPTSVMTRLI LIMVWRKLIR NPNSY SSLF GITWSLISFK WNIEMPALIA KSISILSDAG LGMAMFSLGL FMALNPRIIA CGNRRAAFAA AMRFVVGPAV MLVASY AVG LRGVLLHVAI IQAALPQGIV PFVFAKEYNV HPDILSTAVI FGMLIALPIT LLYYILLGL

UniProtKB: Auxin efflux carrier component 1

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Macromolecule #2: nanobody

MacromoleculeName: nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.36991 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSSSQVQLVE SGGGLVQAGG SLRLSCAASG FPVNISWMEW YRQVPGKERE WVAAIQSTGS YTWYADSVKG RFTISRDNAK NTVYLQMNS LKPEDTAVYY CRVKVGAYYR GQGTQVTVSA GRAG

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Macromolecule #3: 2-(naphthalen-1-ylcarbamoyl)benzoic acid

MacromoleculeName: 2-(naphthalen-1-ylcarbamoyl)benzoic acid / type: ligand / ID: 3 / Number of copies: 2 / Formula: E7O
Molecular weightTheoretical: 291.301 Da
Chemical component information

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

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215094
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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