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Yorodumi- EMDB-33692: Structure of the auxin exporter PIN1 in Arabidopsis thaliana in t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33692 | |||||||||||||||
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Title | Structure of the auxin exporter PIN1 in Arabidopsis thaliana in the NPA-bound state | |||||||||||||||
Map data | EM map | |||||||||||||||
Sample |
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Function / homology | Function and homology information cotyledon morphogenesis / leaf formation / cotyledon development / shoot system development / leaf shaping / xylem and phloem pattern formation / inflorescence development / auxin efflux transmembrane transporter activity / auxin polar transport / auxin export across the plasma membrane ...cotyledon morphogenesis / leaf formation / cotyledon development / shoot system development / leaf shaping / xylem and phloem pattern formation / inflorescence development / auxin efflux transmembrane transporter activity / auxin polar transport / auxin export across the plasma membrane / gravitropism / plant-type cell wall / photomorphogenesis / root development / flower development / auxin-activated signaling pathway / embryo development ending in seed dormancy / 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 | |||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) / Escherichia coli (E. coli) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Sun L / Liu X / Yang Z / Xia J | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33692.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-33692-v30.xml emd-33692.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33692_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_33692.png | 169.1 KB | ||
Others | emd_33692_half_map_1.map.gz emd_33692_half_map_2.map.gz | 59.1 MB 59.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33692 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33692 | HTTPS FTP |
-Validation report
Summary document | emd_33692_validation.pdf.gz | 653.2 KB | Display | EMDB validaton report |
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Full document | emd_33692_full_validation.pdf.gz | 652.8 KB | Display | |
Data in XML | emd_33692_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_33692_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33692 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33692 | HTTPS FTP |
-Related structure data
Related structure data | 7y9uMC 7y9tC 7y9vC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33692.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | EM map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map 1
File | emd_33692_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_33692_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : AtPIN1 in complex with a nanobody and NPA
Entire | Name: AtPIN1 in complex with a nanobody and NPA |
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Components |
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-Supramolecule #1: AtPIN1 in complex with a nanobody and NPA
Supramolecule | Name: AtPIN1 in complex with a nanobody and NPA / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F |
-Supramolecule #2: AtPIN1
Supramolecule | Name: AtPIN1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: nanobody
Supramolecule | Name: nanobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: Auxin efflux carrier component 1
Macromolecule | Name: Auxin efflux carrier component 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 67.080781 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: nanobody
Macromolecule | Name: nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 13.36991 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSSSQVQLVE SGGGLVQAGG SLRLSCAASG FPVNISWMEW YRQVPGKERE WVAAIQSTGS YTWYADSVKG RFTISRDNAK NTVYLQMNS LKPEDTAVYY CRVKVGAYYR GQGTQVTVSA GRAG |
-Macromolecule #3: 2-(naphthalen-1-ylcarbamoyl)benzoic acid
Macromolecule | Name: 2-(naphthalen-1-ylcarbamoyl)benzoic acid / type: ligand / ID: 3 / Number of copies: 2 / Formula: E7O |
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Molecular weight | Theoretical: 291.301 Da |
Chemical component information | ChemComp-E7O: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |