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- EMDB-32570: NPA bound state of AtPIN3 -

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Basic information

Entry
Database: EMDB / ID: EMD-32570
TitleNPA bound state of AtPIN3
Map dataNPA-bound state AtPIN3
Sample
  • Complex: NPA-bound state of AtPIN3(AtPIN3-NPA)
    • Protein or peptide: Auxin efflux carrier component 3
  • Ligand: 2-(naphthalen-1-ylcarbamoyl)benzoic acid
KeywordsPIN-FORMED (PIN) protein / NPA / TRANSPORT PROTEIN
Function / homology
Function and homology information


tropism / root hair initiation / root hair elongation / gravitropism / positive gravitropism / auxin export across the plasma membrane / auxin efflux transmembrane transporter activity / auxin polar transport / root development / auxin-activated signaling pathway ...tropism / root hair initiation / root hair elongation / gravitropism / positive gravitropism / auxin export across the plasma membrane / auxin efflux transmembrane transporter activity / auxin polar transport / 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: 2.62 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: Su N / Zhu A / Tao X / Ding ZJ / Chang S / Ye F / Zhang Y / Zhao C / Chen Q / Wang J / Zhou CY / Guo Y / Jiao S / Zhang S / Wen H / Ma L / Ye S / Zheng SJ / Yang F / Wu S / Guo J
History
DepositionJan 11, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_32570.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNPA-bound state AtPIN3
Voxel sizeX=Y=Z: 0.851 Å
Density
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum-0.14655589 - 0.19539605
Average (Standard dev.)-0.000041331914 (±0.0052337265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 204.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : NPA-bound state of AtPIN3(AtPIN3-NPA)

EntireName: NPA-bound state of AtPIN3(AtPIN3-NPA)
Components
  • Complex: NPA-bound state of AtPIN3(AtPIN3-NPA)
    • Protein or peptide: Auxin efflux carrier component 3
  • Ligand: 2-(naphthalen-1-ylcarbamoyl)benzoic acid

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Supramolecule #1: NPA-bound state of AtPIN3(AtPIN3-NPA)

SupramoleculeName: NPA-bound state of AtPIN3(AtPIN3-NPA) / 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: 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

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.5 sec. / Average electron dose: 54.0 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: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 554149
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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