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- EMDB-23351: Structure of Arabidopsis thaliana sulfate transporter AtSULTR4;1 -

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Basic information

Entry
Database: EMDB / ID: EMD-23351
TitleStructure of Arabidopsis thaliana sulfate transporter AtSULTR4;1
Map data
Sample
  • Complex: Sulfate transporter 4;1
    • Protein or peptide: Sulfate transporter 4.1, chloroplastic
  • Ligand: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
  • Ligand: SULFATE IONSulfate
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: water
KeywordsSulfate transport / SLC26 / MEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


: / chloroplast membrane / secondary active sulfate transmembrane transporter activity / symporter activity / plasma membrane => GO:0005886
Similarity search - Function
Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily
Similarity search - Domain/homology
Sulfate transporter 4.1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsWang L / Chen K
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK122784 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086392 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structure and function of an Arabidopsis thaliana sulfate transporter.
Authors: Lie Wang / Kehan Chen / Ming Zhou /
Abstract: Plant sulfate transporters (SULTR) mediate absorption and distribution of sulfate (SO) and are essential for plant growth; however, our understanding of their structures and functions remains ...Plant sulfate transporters (SULTR) mediate absorption and distribution of sulfate (SO) and are essential for plant growth; however, our understanding of their structures and functions remains inadequate. Here we present the structure of a SULTR from Arabidopsis thaliana, AtSULTR4;1, in complex with SO at an overall resolution of 2.8 Å. AtSULTR4;1 forms a homodimer and has a structural fold typical of the SLC26 family of anion transporters. The bound SO is coordinated by side-chain hydroxyls and backbone amides, and further stabilized electrostatically by the conserved Arg393 and two helix dipoles. Proton and SO are co-transported by AtSULTR4;1 and a proton gradient significantly enhances SO transport. Glu347, which is ~7 Å from the bound SO, is required for H-driven transport. The cytosolic STAS domain interacts with transmembrane domains, and deletion of the STAS domain or mutations to the interface compromises dimer formation and reduces SO transport, suggesting a regulatory function of the STAS domain.
History
DepositionJan 26, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.65
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.65
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lhv
  • Surface level: 0.65
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23351.png

Downloads & links

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Map

FileDownload / File: emd_23351.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.65 / Movie #1: 0.65
Minimum - Maximum-3.6433246 - 5.280939
Average (Standard dev.)-0.00025327437 (±0.16229968)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 206.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z206.000206.000206.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-3.6435.281-0.000

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Supplemental data

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Half map: #2

Fileemd_23351_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_23351_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Sulfate transporter 4;1

EntireName: Sulfate transporter 4;1
Components
  • Complex: Sulfate transporter 4;1
    • Protein or peptide: Sulfate transporter 4.1, chloroplastic
  • Ligand: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
  • Ligand: SULFATE IONSulfate
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: water

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Supramolecule #1: Sulfate transporter 4;1

SupramoleculeName: Sulfate transporter 4;1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 70 KDa

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Macromolecule #1: Sulfate transporter 4.1, chloroplastic

MacromoleculeName: Sulfate transporter 4.1, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 75.168164 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSYASLSVKD LTSLVSRSGT GSSSSLKPPG QTRPVKVIPL QHPDTSNEAR PPSIPFDDIF SGWTAKIKRM RLVDWIDTLF PCFRWIRTY RWSEYFKLDL MAGITVGIML VPQAMSYAKL AGLPPIYGLY SSFVPVFVYA IFGSSRQLAI GPVALVSLLV S NALGGIAD ...String:
MSYASLSVKD LTSLVSRSGT GSSSSLKPPG QTRPVKVIPL QHPDTSNEAR PPSIPFDDIF SGWTAKIKRM RLVDWIDTLF PCFRWIRTY RWSEYFKLDL MAGITVGIML VPQAMSYAKL AGLPPIYGLY SSFVPVFVYA IFGSSRQLAI GPVALVSLLV S NALGGIAD TNEELHIELA ILLALLVGIL ECIMGLLRLG WLIRFISHSV ISGFTSASAI VIGLSQIKYF LGYSIARSSK IV PIVESII AGADKFQWPP FVMGSLILVI LQVMKHVGKA KKELQFLRAA APLTGIVLGT TIAKVFHPPS ISLVGEIPQG LPT FSFPRS FDHAKTLLPT SALITGVAIL ESVGIAKALA AKNRYELDSN SELFGLGVAN ILGSLFSAYP ATGSFSRSAV NNES EAKTG LSGLITGIII GCSLLFLTPM FKYIPQCALA AIVISAVSGL VDYDEAIFLW RVDKRDFSLW TITSTITLFF GIEIG VLVG VGFSLAFVIH ESANPHIAVL GRLPGTTVYR NIKQYPEAYT YNGIVIVRID SPIYFANISY IKDRLREYEV AVDKYT NRG LEVDRINFVI LEMSPVTHID SSAVEALKEL YQEYKTRDIQ LAISNPNKDV HLTIARSGMV ELVGKEWFFV RVHDAVQ VC LQYVQSSNLE DKHLSFTRRY GGSNNNSSSS NALLKEPLLS VEK

UniProtKB: Sulfate transporter 4.1, chloroplastic

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Macromolecule #2: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

MacromoleculeName: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
type: ligand / ID: 2 / Number of copies: 4 / Formula: S1P
Molecular weightTheoretical: 379.472 Da
Chemical component information

ChemComp-S1P:
(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate / Sphingosine-1-phosphate

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Macromolecule #3: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION / Sulfate

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Macromolecule #4: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 4 / Number of copies: 2 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM / POPC

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rtc

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 838096
FSC plot (resolution estimation)

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