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- EMDB-36481: Cryo-EM structure of ClC-6 apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-36481
TitleCryo-EM structure of ClC-6 apo state
Map data
Sample
  • Organelle or cellular component: endolysosomal transporter
    • Protein or peptide: H(+)/Cl(-) exchange transporter 6
  • Ligand: CHLORIDE IONChloride
Keywordsendolysosomal transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


voltage-gated chloride channel activity / cell volume homeostasis / antiporter activity / chloride transmembrane transporter activity / chloride transport / response to mechanical stimulus / monoatomic ion transmembrane transport / Stimuli-sensing channels / Signaling by BRAF and RAF1 fusions / late endosome membrane ...voltage-gated chloride channel activity / cell volume homeostasis / antiporter activity / chloride transmembrane transporter activity / chloride transport / response to mechanical stimulus / monoatomic ion transmembrane transport / Stimuli-sensing channels / Signaling by BRAF and RAF1 fusions / late endosome membrane / endosome membrane / lysosomal membrane / intracellular membrane-bounded organelle / signal transduction / ATP binding / membrane
Similarity search - Function
Chloride channel ClC-6 / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
H(+)/Cl(-) exchange transporter 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang SS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030056 China
CitationJournal: Sci Adv / Year: 2023
Title: Molecular basis of ClC-6 function and its impairment in human disease
Authors: Zhang SS
History
DepositionJun 12, 2023-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36481.png

Downloads & links

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Map

FileDownload / File: emd_36481.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8374 Å
Density
Contour LevelBy AUTHOR: 0.436
Minimum - Maximum-1.385509 - 2.5903473
Average (Standard dev.)0.00511107 (±0.06960127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 267.96802 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36481_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36481_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 : endolysosomal transporter

EntireName: endolysosomal transporter
Components
  • Organelle or cellular component: endolysosomal transporter
    • Protein or peptide: H(+)/Cl(-) exchange transporter 6
  • Ligand: CHLORIDE IONChloride

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Supramolecule #1: endolysosomal transporter

SupramoleculeName: endolysosomal transporter / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: H(+)/Cl(-) exchange transporter 6

MacromoleculeName: H(+)/Cl(-) exchange transporter 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.38343 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGCRGSLCC CCRWCCCCGE RETRTPEELT ILGETQEEED EILPRKDYES LDYDRCINDP YLEVLETMDN KKGRRYEAVK WMVVFAIGV CTGLVGLFVD FFVRLFTQLK FGVVQTSVEE CSQKGCLALS LLELLGFNLT FVFLASLLVL IEPVAAGSGI P EVKCYLNG ...String:
MAGCRGSLCC CCRWCCCCGE RETRTPEELT ILGETQEEED EILPRKDYES LDYDRCINDP YLEVLETMDN KKGRRYEAVK WMVVFAIGV CTGLVGLFVD FFVRLFTQLK FGVVQTSVEE CSQKGCLALS LLELLGFNLT FVFLASLLVL IEPVAAGSGI P EVKCYLNG VKVPGIVRLR TLLCKVLGVL FSVAGGLFVE KEGPMIHSGS VVGAGLPQFQ SISLRKIQFN FPYFRSDRDK RD FVSAGAA AGVAAAFGAP IGGTLFSLEE GSSFWNQGLT WKVLFCSMSA TFTLNFFRSG IQFGSWGSFQ LPGLLNFGEF KCS DSDKKC HLWTAMDLGF FVVMGVIGGL LGATFNCLNK RLAKYRMRNV HPKPKLVRVL ESLLVSLVTT VVVFVASMVL GECR QMSSS SQIGNDSFQL QVTEDVNSSI KTFFCPNDTY NDMATLFFNP QESAILQLFH QDGTFSPVTL ALFFVLYFLL ACWTY GISV PSGLFVPSLL CGAAFGRLVA NVLKSYIGLG HIYSGTFALI GAAAFLGGVV RMTISLTVIL IESTNEITYG LPIMVT LMV AKWTGDFFNK GIYDIHVGLR GVPLLEWETE VEMDKLRASD IMEPNLTYVY PHTRIQSLVS ILRTTVHHAF PVVTENR GN EKEFMKGNQL ISNNIKFKKS SILTRAGEQR KRSQSMKSYP SSELRNMCDE HIASEEPAEK EDLLQQMLER RYTPYPNL Y PDQSPSEDWT MEERFRPLTF HGLILRSQLV TLLVRGVCYS ESQSSASQPR LSYAEMAEDY PRYPDIHDLD LTLLNPRMI VDVTPYMNPS PFTVSPNTHV SQVFNLFRTM GLRHLPVVNA VGEIVGIITR HNLTYEFLQA RLRQHYQTI

UniProtKB: H(+)/Cl(-) exchange transporter 6

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Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 182000

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