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- EMDB-33088: Structure of Arabidopsis thaliana CLCa -

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Basic information

Entry
Database: EMDB / ID: EMD-33088
TitleStructure of Arabidopsis thaliana CLCa
Map data
Sample
  • Complex: AtCLCa
    • Protein or peptide: Chloride channel protein CLC-a
  • Ligand: NITRATE ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsnitrate / antiporter / transport protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


nitrate transmembrane transporter activity / nitrate transmembrane transport / response to nitrate / voltage-gated chloride channel activity / chloride transport / chloride channel complex
Similarity search - Function
Chloride channel ClC-plant / : / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
Chloride channel protein CLC-a
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsJi S / Jin H / Kaiming Z / Mingxing W / Shanshan L / Long C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071201 China
CitationJournal: J Biol Chem / Year: 2023
Title: Cryo-EM structure of the plant nitrate transporter AtCLCa reveals characteristics of the anion-binding site and the ATP-binding pocket.
Authors: Jin He / Mingxing Wang / Shanshan Li / Long Chen / Kaiming Zhang / Ji She /
Abstract: Nitrate is one of the major nitrogen sources for most plants. Chloride channel (CLC) proteins mediate the transport and vacuole storage of nitrate in plants, but the structural basis of nitrate ...Nitrate is one of the major nitrogen sources for most plants. Chloride channel (CLC) proteins mediate the transport and vacuole storage of nitrate in plants, but the structural basis of nitrate transport by plant CLC proteins remains unknown. Here, we solved the cryo-EM structure of ATP-bound Arabidopsis thaliana CLCa (AtCLCa) at 2.8 Å resolution. Structural comparison between nitrate-selective AtCLCa and chloride-selective CLC-7 reveals key differences in the central anion-binding site. We observed that the central nitrate is shifted by ∼1.4 Å from chloride, which is likely caused by a weaker interaction between the anion and Pro160; the side chains of aromatic residues around the central binding site are rearranged to accommodate the larger nitrate. Additionally, we identified the ATP-binding pocket of AtCLCa to be located between the cytosolic cystathionine β-synthase domains and the N-terminus. The N-terminus may mediate the ATP inhibition of AtCLCa by interacting with both ATP and the pore-forming transmembrane helix. Together, our studies provide insights into the nitrate selectivity and ATP regulation of plant CLCs.
History
DepositionMar 17, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33088.png

Downloads & links

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Map

FileDownload / File: emd_33088.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.3140209 - 2.1353185
Average (Standard dev.)-0.00016691856 (±0.026227526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33088_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram (log scale)

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Half map: #1

Fileemd_33088_half_map_2.map
Projections & Slices
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Sample components

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Entire : AtCLCa

EntireName: AtCLCa
Components
  • Complex: AtCLCa
    • Protein or peptide: Chloride channel protein CLC-a
  • Ligand: NITRATE ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: AtCLCa

SupramoleculeName: AtCLCa / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Chloride channel protein CLC-a

MacromoleculeName: Chloride channel protein CLC-a / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 88.17682 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDEDGNLQIS NSNYNGEEEG EDPENNTLNQ PLLKRHRTLS STPLALVGAK VSHIESLDYE INENDLFKHD WRSRSKAQVF QYIFLKWTL ACLVGLFTGL IATLINLAVE NIAGYKLLAV GYYIAQDRFW TGLMVFTGAN LGLTLVATVL VVYFAPTAAG P GIPEIKAY ...String:
MDEDGNLQIS NSNYNGEEEG EDPENNTLNQ PLLKRHRTLS STPLALVGAK VSHIESLDYE INENDLFKHD WRSRSKAQVF QYIFLKWTL ACLVGLFTGL IATLINLAVE NIAGYKLLAV GYYIAQDRFW TGLMVFTGAN LGLTLVATVL VVYFAPTAAG P GIPEIKAY LNGIDTPNMF GFTTMMVKIV GSIGAVAAGL DLGKEGPLVH IGSCIASLLG QGGPDNHRIK WRWLRYFNND RD RRDLITC GSASGVCAAF RSPVGGVLFA LEEVATWWRS ALLWRTFFST AVVVVVLRAF IEICNSGKCG LFGSGGLIMF DVS HVEVRY HAADIIPVTL IGVFGGILGS LYNHLLHKVL RLYNLINQKG KIHKVLLSLG VSLFTSVCLF GLPFLAECKP CDPS IDEIC PTNGRSGNFK QFNCPNGYYN DLSTLLLTTN DDAVRNIFSS NTPNEFGMVS LWIFFGLYCI LGLITFGIAT PSGLF LPII LMGSAYGRML GTAMGSYTNI DQGLYAVLGA ASLMAGSMRM TVSLCVIFLE LTNNLLLLPI TMFVLLIAKT VGDSFN LSI YEIILHLKGL PFLEANPEPW MRNLTVGELN DAKPPVVTLN GVEKVANIVD VLRNTTHNAF PVLDGADQNT GTELHGL IL RAHLVKVLKK RWFLNEKRRT EEWEVREKFT PVELAEREDN FDDVAITSSE MQLYVDLHPL TNTTPYTVVQ SMSVAKAL V LFRSVGLRHL LVVPKIQASG MSPVIGILTR QDLRAYNILQ AFPHLDKHKS GKARASGGSL EVLFQGPGGS GGSWSHPQF EK

UniProtKB: Chloride channel protein CLC-a

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Macromolecule #2: NITRATE ION

MacromoleculeName: NITRATE ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: NO3
Molecular weightTheoretical: 62.005 Da
Chemical component information

ChemComp-NO3:
NITRATE ION

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7jm6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2913673
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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