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- EMDB-31167: Cryo-EM structure of VCCN1 Y332A mutant in lipid nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-31167
TitleCryo-EM structure of VCCN1 Y332A mutant in lipid nanodisc
Map data
Sample
  • Complex: Bestrophin-like protein
    • Protein or peptide: Bestrophin-like protein
KeywordsIon channel / Thylakoid / Photosynthesis / Bestrophin family / MEMBRANE PROTEIN
Function / homologyUPF0187 protein At3g61320-like / regulation of photosynthesis, light reaction / UPF0187 family / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / voltage-gated chloride channel activity / membrane / Uncharacterized protein
Function and homology information
Biological speciesMalus domestica (apple)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsHagino T / Kato T / Kasuya G / Kobayashi K / Kusakizako T / Yamashita K / Nishizawa T / Nureki O
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structures of thylakoid-located voltage-dependent chloride channel VCCN1.
Authors: Tatsuya Hagino / Takafumi Kato / Go Kasuya / Kan Kobayashi / Tsukasa Kusakizako / Shin Hamamoto / Tomoaki Sobajima / Yuichiro Fujiwara / Keitaro Yamashita / Hisashi Kawasaki / Andrés D ...Authors: Tatsuya Hagino / Takafumi Kato / Go Kasuya / Kan Kobayashi / Tsukasa Kusakizako / Shin Hamamoto / Tomoaki Sobajima / Yuichiro Fujiwara / Keitaro Yamashita / Hisashi Kawasaki / Andrés D Maturana / Tomohiro Nishizawa / Osamu Nureki /
Abstract: In the light reaction of plant photosynthesis, modulation of electron transport chain reactions is important to maintain the efficiency of photosynthesis under a broad range of light intensities. ...In the light reaction of plant photosynthesis, modulation of electron transport chain reactions is important to maintain the efficiency of photosynthesis under a broad range of light intensities. VCCN1 was recently identified as a voltage-gated chloride channel residing in the thylakoid membrane, where it plays a key role in photoreaction tuning to avoid the generation of reactive oxygen species (ROS). Here, we present the cryo-EM structures of Malus domestica VCCN1 (MdVCCN1) in nanodiscs and detergent at 2.7 Å and 3.0 Å resolutions, respectively, and the structure-based electrophysiological analyses. VCCN1 structurally resembles its animal homolog, bestrophin, a Ca-gated anion channel. However, unlike bestrophin channels, VCCN1 lacks the Ca-binding motif but instead contains an N-terminal charged helix that is anchored to the lipid membrane through an additional amphipathic helix. Electrophysiological experiments demonstrate that these structural elements are essential for the channel activity, thus revealing the distinct activation mechanism of VCCN1.
History
DepositionApr 3, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31167.png

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Map

FileDownload / File: emd_31167.map.gz / Format: CCP4 / Size: 6.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 122 pix.
= 162.016 Å		1.33 Å/pix.
x 122 pix.
= 162.016 Å		1.33 Å/pix.
x 122 pix.
= 162.016 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.328 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.054
Minimum - Maximum-0.16939624 - 0.31304598
Average (Standard dev.)0.0011297051 (±0.017600171)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions122122122
Spacing122122122
CellA=B=C: 162.01599 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_31167_msk_1.map
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Half map: #2

Fileemd_31167_half_map_1.map
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Half map: #1

Fileemd_31167_half_map_2.map
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Sample components

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Entire : Bestrophin-like protein

EntireName: Bestrophin-like protein
Components
  • Complex: Bestrophin-like protein
    • Protein or peptide: Bestrophin-like protein

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Supramolecule #1: Bestrophin-like protein

SupramoleculeName: Bestrophin-like protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Malus domestica (apple)

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Macromolecule #1: Bestrophin-like protein

MacromoleculeName: Bestrophin-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Malus domestica (apple)
Molecular weightTheoretical: 41.965645 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPNPSPPSSS SPVQTLISIL RIIPDWSDRT QERGMRQHRT LYDHEKWMHH RSSYRHLRHL LSSLSSRVIL SLIPPVIAFT LVAVVIASY NTAVALDLLP GIFPLLRSSS LPYQLTAPAL ALLLVFRTEA SYSRFEEGRK SWTEVIAGAN DFARQIISSV E TSGDAQLK ...String:
MPNPSPPSSS SPVQTLISIL RIIPDWSDRT QERGMRQHRT LYDHEKWMHH RSSYRHLRHL LSSLSSRVIL SLIPPVIAFT LVAVVIASY NTAVALDLLP GIFPLLRSSS LPYQLTAPAL ALLLVFRTEA SYSRFEEGRK SWTEVIAGAN DFARQIISSV E TSGDAQLK KALLQYIVAF PVALKCHVIY GSDIARDLQN LLEVDDLLVV LNSKHRPGCI IQFISRSLQL LKLEESRRIM LQ SKISCFH EGIGICEQLI GTPIPLSATR LTSRFLVLWH LTLPIILWDD CHWIVVPATF ISAASLFCIE QVGVLIEEPF PML ALDDLC NSVRNNVQEA LASEKLIRAR LAAKGRIQSE QQFQNGQPRP ENLYFQ

UniProtKB: Uncharacterized protein

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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 / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2835 / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 107192
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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