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- EMDB-32328: Cryo-EM structure of GmALMT12/QUAC1 anion channel -

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Basic information

Entry
Database: EMDB / ID: EMD-32328
TitleCryo-EM structure of GmALMT12/QUAC1 anion channel
Map dataHalf map 2 for GmALMT12/QUAC1
Sample
  • Organelle or cellular component: GmALMT12/QUAC1
    • Protein or peptide: GmALMT12/QUAC1
KeywordsSymmetrical dimer / T-shaped pore / twisted two-layer architecture / Malate-modulation / MEMBRANE PROTEIN
Function / homologymalate transport / Aluminum-activated malate transporter / Aluminium activated malate transporter / plant-type vacuole membrane / Aluminum-activated malate transporter 12
Function and homology information
Biological speciesGlycine max (soybean)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsQin L / Tang LH
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509903, 2016YFA0500503, 2017YFA0504703 China
Chinese Academy of SciencesXDA24020305, XDB37040102, 153E11KYSB20190029 China
National Natural Science Foundation of China (NSFC)31872721, 31771566 China
CitationJournal: Sci Adv / Year: 2022
Title: Cryo-EM structure and electrophysiological characterization of ALMT from reveal a previously uncharacterized class of anion channels.
Authors: Li Qin / Ling-Hui Tang / Jia-Shu Xu / Xian-Hui Zhang / Yun Zhu / Chun-Rui Zhang / Mei-Hua Wang / Xue-Lei Liu / Fei Li / Fei Sun / Min Su / Yujia Zhai / Yu-Hang Chen /
Abstract: Aluminum-activated malate transporters (ALMTs) form an anion channel family that plays essential roles in diverse functions in plants. ALMT12, also named QUAC1 (quick anion channel 1), regulates ...Aluminum-activated malate transporters (ALMTs) form an anion channel family that plays essential roles in diverse functions in plants. ALMT12, also named QUAC1 (quick anion channel 1), regulates stomatal closure in response to environmental stimuli. However, the molecular basis of ALMT12/QUAC1 activity remains elusive. Here, we describe the cryo-EM structure of ALMT12/QUAC1 from at 3.5-Å resolution. ALMT12/QUAC1 is a symmetrical dimer, forming a single electropositive T-shaped pore across the membrane. The transmembrane and cytoplasmic domains are assembled into a twisted two-layer architecture, with their associated dimeric interfaces nearly perpendicular. ALMT12/QUAC1-mediated currents display rapid kinetics of activation/deactivation and a bell-shaped voltage dependency, reminiscent of the rapid (R)-type anion currents. Our structural and functional analyses reveal a domain-twisting mechanism for malate-mediated activation. Together, our study uncovers the molecular basis for a previously uncharacterized class of anion channels and provides insights into the gating and modulation of the ALMT12/QUAC1 anion channel.
History
DepositionDec 1, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.33
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.33
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7w6k
  • Surface level: 0.33
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32328.png

Downloads & links

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Map

FileDownload / File: emd_32328.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHalf map 2 for GmALMT12/QUAC1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 224 pix.
= 232.96 Å		1.04 Å/pix.
x 224 pix.
= 232.96 Å		1.04 Å/pix.
x 224 pix.
= 232.96 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33 / Movie #1: 0.33
Minimum - Maximum-0.6240015 - 1.2380936
Average (Standard dev.)0.0020018986 (±0.040889483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 232.95999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z232.960232.960232.960
α/β/γ90.00090.00090.000
start NX/NY/NZ139118109
NX/NY/NZ123164187
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.6241.2380.002

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Supplemental data

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Additional map: Sharpen map for GmALMT12/QUAC1

Fileemd_32328_additional_1.map
AnnotationSharpen map for GmALMT12/QUAC1
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Reconstructed Density map for GmALMT12/QUAC1

Fileemd_32328_half_map_1.map
AnnotationReconstructed Density map for GmALMT12/QUAC1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 for GmALMT12/QUAC1

Fileemd_32328_half_map_2.map
AnnotationHalf map 1 for GmALMT12/QUAC1
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GmALMT12/QUAC1

EntireName: GmALMT12/QUAC1
Components
  • Organelle or cellular component: GmALMT12/QUAC1
    • Protein or peptide: GmALMT12/QUAC1

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Supramolecule #1: GmALMT12/QUAC1

SupramoleculeName: GmALMT12/QUAC1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Glycine max (soybean)

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Macromolecule #1: GmALMT12/QUAC1

MacromoleculeName: GmALMT12/QUAC1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Glycine max (soybean)
Molecular weightTheoretical: 60.321969 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe (fission yeast)
SequenceString: MVPKVYAGQE MAMVENENCI MNGKWKKRVH VFGERVMRFP NKAWQTTWKV GREDPRRLIH AFKVGLSLTL ASLLYLLEPL FKGIGQSAI WAVMTVVVVL EFTAGATLCK GLNRGLGTLL AGLLAFLVGY IANASDRVSQ AIIIGAAVFF IGALATYMRF I PYIKKNYD ...String:
MVPKVYAGQE MAMVENENCI MNGKWKKRVH VFGERVMRFP NKAWQTTWKV GREDPRRLIH AFKVGLSLTL ASLLYLLEPL FKGIGQSAI WAVMTVVVVL EFTAGATLCK GLNRGLGTLL AGLLAFLVGY IANASDRVSQ AIIIGAAVFF IGALATYMRF I PYIKKNYD YGLVIFLLTF NLITVSSYRL ENVLKIAHDR VYTIAIGCAV CLLMSLLVFP NWSGEDLHNS TVYKLEGLAK SI EACVNEY FYGEIEGSGY MKLSEDPIYK GYKAVLDSKS IDETLALHAS WEPRHSRYCH RFPWQQYVKV GAVLRQFGYT VVA LHGCLR TEIQTPRSVR AMFKDPCIRL AAEVSKVLIE LSNSIRNRRH CSPEILSDHL HEALQDLNTA IKSQPRLFLG PKHR HNQAT NMLKIAAAQV GQERHGKTSL SSVKTDSSAL LEWKTKRVSA EQTKESERKS LRPQLSKIAI TSLEFSEALP FAAFA SLLV ETVAKLDLVI EEVEELGRLA CFKEFIPGDE FVVTCQEPRV DVSQNHLPSH GVD

UniProtKB: Aluminum-activated malate transporter 12

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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

Concentration5 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 6189 / Average exposure time: 8.0 sec. / 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 / Cs: 2.7 mm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2987283
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 169576
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7w6k:
Cryo-EM structure of GmALMT12/QUAC1 anion channel

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