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- EMDB-36487: Cryo-EM structure of Y553C human ClC-6 -

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Basic information

Entry
Database: EMDB / ID: EMD-36487
TitleCryo-EM structure of Y553C human ClC-6
Map data
Sample
  • Organelle or cellular component: endolysosomal transporter
    • Protein or peptide: H(+)/Cl(-) exchange transporter 6
  • Ligand: CHLORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


voltage-gated chloride channel activity / cell volume homeostasis / chloride transport / chloride transmembrane transporter activity / antiporter activity / response to mechanical stimulus / Stimuli-sensing channels / late endosome membrane / Signaling by BRAF and RAF1 fusions / monoatomic ion transmembrane transport ...voltage-gated chloride channel activity / cell volume homeostasis / chloride transport / chloride transmembrane transporter activity / antiporter activity / response to mechanical stimulus / Stimuli-sensing channels / late endosome membrane / Signaling by BRAF and RAF1 fusions / monoatomic ion transmembrane transport / 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 / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / 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: 3.4 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-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36487.png

Downloads & links

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Map

FileDownload / File: emd_36487.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 280 pix.
= 234.472 Å		0.84 Å/pix.
x 280 pix.
= 234.472 Å		0.84 Å/pix.
x 280 pix.
= 234.472 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8374 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.322
Minimum - Maximum-0.9141033 - 1.5984055
Average (Standard dev.)0.0068459935 (±0.05769508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 234.472 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36487_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_36487_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 ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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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: 97.323398 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 IESTNEITCG 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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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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