[English] 日本語
Yorodumi
- EMDB-4747: CryoEM structure of calcium-bound human TMEM16K / Anoctamin 10 in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4747
TitleCryoEM structure of calcium-bound human TMEM16K / Anoctamin 10 in detergent (low Ca2+, closed form)
Map dataRELION3 postprocessed map sharpened with a bfactor of -176A**2
Sample
  • Organelle or cellular component: Anoctamin 10Calcium-dependent chloride channel
    • Protein or peptide: Anoctamin-10Calcium-dependent chloride channel
  • Ligand: CALCIUM IONCalcium
Function / homology
Function and homology information


intracellularly calcium-gated chloride channel activity / calcium-activated cation channel activity / chloride transport / chloride channel activity / monoatomic cation transport / chloride transmembrane transport / monoatomic ion transmembrane transport / Stimuli-sensing channels / Induction of Cell-Cell Fusion / intracellular membrane-bounded organelle ...intracellularly calcium-gated chloride channel activity / calcium-activated cation channel activity / chloride transport / chloride channel activity / monoatomic cation transport / chloride transmembrane transport / monoatomic ion transmembrane transport / Stimuli-sensing channels / Induction of Cell-Cell Fusion / intracellular membrane-bounded organelle / membrane / plasma membrane
Similarity search - Function
Anoctamin / Calcium-activated chloride channel
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsPike ACW / Bushell SR / Shintre CA / Tessitore A / Chu A / Mukhopadhyay S / Shrestha L / Chalk R / Burgess-Brown NA / Love J ...Pike ACW / Bushell SR / Shintre CA / Tessitore A / Chu A / Mukhopadhyay S / Shrestha L / Chalk R / Burgess-Brown NA / Love J / Huiskonen JT / Edwards AM / Arrowsmith CH / Bountra C / Carpenter EP / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/Z United Kingdom
European Commission115766 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: The structural basis of lipid scrambling and inactivation in the endoplasmic reticulum scramblase TMEM16K.
Authors: Simon R Bushell / Ashley C W Pike / Maria E Falzone / Nils J G Rorsman / Chau M Ta / Robin A Corey / Thomas D Newport / John C Christianson / Lara F Scofano / Chitra A Shintre / Annamaria ...Authors: Simon R Bushell / Ashley C W Pike / Maria E Falzone / Nils J G Rorsman / Chau M Ta / Robin A Corey / Thomas D Newport / John C Christianson / Lara F Scofano / Chitra A Shintre / Annamaria Tessitore / Amy Chu / Qinrui Wang / Leela Shrestha / Shubhashish M M Mukhopadhyay / James D Love / Nicola A Burgess-Brown / Rebecca Sitsapesan / Phillip J Stansfeld / Juha T Huiskonen / Paolo Tammaro / Alessio Accardi / Elisabeth P Carpenter /
Abstract: Membranes in cells have defined distributions of lipids in each leaflet, controlled by lipid scramblases and flip/floppases. However, for some intracellular membranes such as the endoplasmic ...Membranes in cells have defined distributions of lipids in each leaflet, controlled by lipid scramblases and flip/floppases. However, for some intracellular membranes such as the endoplasmic reticulum (ER) the scramblases have not been identified. Members of the TMEM16 family have either lipid scramblase or chloride channel activity. Although TMEM16K is widely distributed and associated with the neurological disorder autosomal recessive spinocerebellar ataxia type 10 (SCAR10), its location in cells, function and structure are largely uncharacterised. Here we show that TMEM16K is an ER-resident lipid scramblase with a requirement for short chain lipids and calcium for robust activity. Crystal structures of TMEM16K show a scramblase fold, with an open lipid transporting groove. Additional cryo-EM structures reveal extensive conformational changes from the cytoplasmic to the ER side of the membrane, giving a state with a closed lipid permeation pathway. Molecular dynamics simulations showed that the open-groove conformation is necessary for scramblase activity.
History
DepositionMar 29, 2019-
Header (metadata) releaseMay 1, 2019-
Map releaseMay 1, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6r7y
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_4747.map.gz / Format: CCP4 / Size: 45.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRELION3 postprocessed map sharpened with a bfactor of -176A**2
Voxel sizeX=Y=Z: 0.822 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.05866984 - 0.083611496
Average (Standard dev.)0.00012997609 (±0.003871906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions228228228
Spacing228228228
CellA=B=C: 187.416 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z228228228
origin x/y/z0.0000.0000.000
length x/y/z187.416187.416187.416
α/β/γ90.00090.00090.000
start NX/NY/NZ929262
NX/NY/NZ290290360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS228228228
D min/max/mean-0.0590.0840.000

-
Supplemental data

-
Mask #1

Fileemd_4747_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: RELION3 halfmap1

Fileemd_4747_half_map_1.map
AnnotationRELION3 halfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: RELION3 halfmap2

Fileemd_4747_half_map_2.map
AnnotationRELION3 halfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire : Anoctamin 10

EntireName: Anoctamin 10Calcium-dependent chloride channel
Components
  • Organelle or cellular component: Anoctamin 10Calcium-dependent chloride channel
    • Protein or peptide: Anoctamin-10Calcium-dependent chloride channel
  • Ligand: CALCIUM IONCalcium

-
Supramolecule #1: Anoctamin 10

SupramoleculeName: Anoctamin 10 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 153 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant plasmid: PFB-CT10HF-LIC

-
Macromolecule #1: Anoctamin-10

MacromoleculeName: Anoctamin-10 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.276016 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKVTLSALDT SESSFTPLVV IELAQDVKEE TKEWLKNRII AKKKDGGAQL LFRPLLNKYE QETLENQNLY LVGASKIRML LGAEAVGLV KECNDNTMRA FTYRTRQNFK GFDDNNDDFL TMAECQFIIK HELENLRAKD EKMIPGYPQA KLYPGKSLLR R LLTSGIVI ...String:
MKVTLSALDT SESSFTPLVV IELAQDVKEE TKEWLKNRII AKKKDGGAQL LFRPLLNKYE QETLENQNLY LVGASKIRML LGAEAVGLV KECNDNTMRA FTYRTRQNFK GFDDNNDDFL TMAECQFIIK HELENLRAKD EKMIPGYPQA KLYPGKSLLR R LLTSGIVI QVFPLHDSEA LKKLEDTWYT RFALKYQPID SIRGYFGETI ALYFGFLEYF TFALIPMAVI GLPYYLFVWE DY DKYVIFA SFNLIWSTVI LELWKRGCAN MTYRWGTLLM KRKFEEPRPG FHGVLGINSI TGKEEPLYPS YKRQLRIYLV SLP FVCLCL YFSLYVMMIY FDMEVWALGL HENSGSEWTS VLLYVPSIIY AIVIEIMNRL YRYAAEFLTS WENHRLESAY QNHL ILKVL VFNFLNCFAS LFYIAFVLKD MKLLRQSLAT LLITSQILNQ IMESFLPYWL QRKHGVRVKR KVQALKADID ATLYE QVIL EKEMGTYLGT FDDYLELFLQ FGYVSLFSCV YPLAAAFAVL NNFTEVNSDA LKMCRVFKRP FSEPSANIGV WQLAFE TMS VISVVTNCAL IGMSPQVNAV FPESKADLIL IVVAVEHALL ALKFILAFAI PDKPRHIQMK LARLEFESLE ALKQQQM KL VTENLKEEPM ESGKEKATAE NLYFQ

-
Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMC8H18N2O4SNa HEPES
0.045 % (w/v)C23H44O11Undecyl b-D Maltopyranoside
0.0045 % (w/v)C31H50O4cholesteryl hemisuccinate

Details: No additional calcium added. Background levels of calcium estimated to be ca. 500nM
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4.5sec prior to plunging.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.0 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-20 / Number grids imaged: 1 / Number real images: 1975 / Average exposure time: 8.0 sec. / Average electron dose: 56.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 102669
Details: Particles count after a single round of 2D classification
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.5)
Startup modelType of model: OTHER / Details: Ab-initio model calculated in RELION3
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 19000 / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 53880
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsRefined using phenix.real_space_refine with NCS constraints and model reference restraints used (PDB id: TBC) against RELION3 post-processed map.
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 176 / Target criteria: Correlation coef
Output model

PDB-6r7y:
CryoEM structure of calcium-bound human TMEM16K / Anoctamin 10 in detergent (low Ca2+, closed form)

+
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