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- EMDB-33223: TMD masked refine map of human ClC-2 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-33223
TitleTMD masked refine map of human ClC-2
Map data
Sample
  • Complex: Full length human CLC-2 homo dimer
    • Protein or peptide: Chloride channel protein 2
Keywordshomo-dimer / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of aldosterone biosynthetic process / cell differentiation involved in salivary gland development / acinar cell differentiation / voltage-gated chloride channel activity / chloride transport / positive regulation of oligodendrocyte differentiation / chloride channel complex / lung development / Stimuli-sensing channels / retina development in camera-type eye ...regulation of aldosterone biosynthetic process / cell differentiation involved in salivary gland development / acinar cell differentiation / voltage-gated chloride channel activity / chloride transport / positive regulation of oligodendrocyte differentiation / chloride channel complex / lung development / Stimuli-sensing channels / retina development in camera-type eye / perikaryon / dendrite / plasma membrane
Similarity search - Function
Chloride channel ClC-2 / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / CBS domain superfamily / CBS domain profile.
Similarity search - Domain/homology
Chloride channel protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structures of ClC-2 chloride channel reveal the blocking mechanism of its specific inhibitor AK-42
Authors: Ma T / Wang L / Chai A / Liu C / Cui W / Yuan S / Wing Ngor Au S / Sun L / Zhang X / Zhang Z / Lu J / Gao Y / Wang P / Li Z / Liang Y / Vogel H / Wang YT / Wang D / Yan K / Zhang H
History
DepositionApr 15, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33223.png

Downloads & links

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Map

FileDownload / File: emd_33223.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.829 Å
Density
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.06567743 - 0.11030636
Average (Standard dev.)0.00015816325 (±0.0029565145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.224 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33223_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33223_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full length human CLC-2 homo dimer

EntireName: Full length human CLC-2 homo dimer
Components
  • Complex: Full length human CLC-2 homo dimer
    • Protein or peptide: Chloride channel protein 2

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Supramolecule #1: Full length human CLC-2 homo dimer

SupramoleculeName: Full length human CLC-2 homo dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 180 kDa/nm

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Macromolecule #1: Chloride channel protein 2

MacromoleculeName: Chloride channel protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.642352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAAAEEGM EPRALQYEQT LMYGRYTQDL GAFAKEEAAR IRLGGPEPWK GPPSSRAAPE LLEYGRSRCA RCRVCSVRCH KFLVSRVGE DWIFLVLLGL LMALVSWVMD YAIAACLQAQ QWMSRGLNTS ILLQYLAWVT YPVVLITFSA GFTQILAPQA V GSGIPEMK ...String:
MAAAAAEEGM EPRALQYEQT LMYGRYTQDL GAFAKEEAAR IRLGGPEPWK GPPSSRAAPE LLEYGRSRCA RCRVCSVRCH KFLVSRVGE DWIFLVLLGL LMALVSWVMD YAIAACLQAQ QWMSRGLNTS ILLQYLAWVT YPVVLITFSA GFTQILAPQA V GSGIPEMK TILRGVVLKE YLTLKTFIAK VIGLTCALGS GMPLGKEGPF VHIASMCAAL LSKFLSLFGG IYENESRNTE ML AAACAVG VGCCFAAPIG GVLFSIEVTS TFFAVRNYWR GFFAATFSAF IFRVLAVWNR DEETITALFK TRFRLDFPFD LQE LPAFAV IGIASGFGGA LFVYLNRKIV QVMRKQKTIN RFLMRKRLLF PALVTLLIST LTFPPGFGQF MAGQLSQKET LVTL FDNRT WVRQGLVEEL EPPSTSQAWN PPRANVFLTL VIFILMKFWM SALATTIPVP CGAFMPVFVI GAAFGRLVGE SMAAW FPDG IHTDSSTYRI VPGGYAVVGA AALAGAVTHT VSTAVIVFEL TGQIAHILPV MIAVILANAV AQSLQPSLYD SIIRIK KLP YLPELGWGRH QQYRVRVEDI MVRDVPHVAL SCTFRDLRLA LHRTKGRMLA LVESPESMIL LGSIERSQVV ALLGAQL SP ARRRQHMQER RATQTSPLSD QEGPPTPEAS VCFQVNTEDS AFPAARGETH KPLKPALKRG PSVTRNLGES PTGSAESA G IALRSLFCGS PPPEAASEKL ESCEKRKLKR VRISLASDAD LEGEMSPEEI LEWEEQQLDE PVNFSDCKID PAPFQLVER TSLHKTHTIF SLLGVDHAYV TSIGRLIGIV TLKELRKAIE GSVTAQGVKV RPPLASFRDS ATSSSDTETT EVHALWGPHS RHGLPREGS PSDSDDKCQ

UniProtKB: Chloride channel protein 2

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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: 7.4
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43510
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7xja:
TMD masked refine map of human ClC-2

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