[English] 日本語
Yorodumi
- EMDB-31167: Cryo-EM structure of VCCN1 Y332A mutant in lipid nanodisc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31167

*YMImages and movies for this entry are currently under preparation

TitleCryo-EM structure of VCCN1 Y332A mutant in lipid nanodisc
Map data
Sample
  • Complex: Bestrophin-like protein
    • Protein or peptide: Bestrophin-like protein
Function / homologyregulation of photosynthesis, light reaction / UPF0187 protein At3g61320-like / UPF0187 family / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / voltage-gated chloride channel activity / integral component of 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-
UpdateMay 18, 2022-
Current statusMay 18, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

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

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.328 Å
Density
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 °

-
Supplemental data

-
Mask #1

Fileemd_31167_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #2

Fileemd_31167_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_31167_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire : Bestrophin-like protein

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

-
Supramolecule #1: Bestrophin-like protein

SupramoleculeName: Bestrophin-like protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Malus domestica (apple)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
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
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more