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- EMDB-41127: Cryo-EM structure of the human CLC-2 chloride channel transmembra... -
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Open data
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Basic information
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Title | Cryo-EM structure of the human CLC-2 chloride channel transmembrane domain Apo state with resolved N-terminal hairpin | |||||||||||||||
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![]() | Chloride / Channel / Inhibitor / Protein / Voltage gated / TRANSPORT PROTEIN | |||||||||||||||
Function / homology | ![]() regulation of aldosterone biosynthetic process / cell differentiation involved in salivary gland development / astrocyte end-foot / acinar cell differentiation / voltage-gated chloride channel activity / chloride transport / positive regulation of oligodendrocyte differentiation / phagocytosis, engulfment / chloride channel complex / lung development ...regulation of aldosterone biosynthetic process / cell differentiation involved in salivary gland development / astrocyte end-foot / acinar cell differentiation / voltage-gated chloride channel activity / chloride transport / positive regulation of oligodendrocyte differentiation / phagocytosis, engulfment / chloride channel complex / lung development / Stimuli-sensing channels / myelin sheath / retina development in camera-type eye / basolateral plasma membrane / perikaryon / dendrite / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.46 Å | |||||||||||||||
![]() | Xu M / Neelands T / Powers AS / Liu Y / Miller S / Pintilie G / Du Bois J / Dror RO / Chiu W / Maduke M | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism. Authors: Mengyuan Xu / Torben Neelands / Alexander S Powers / Yan Liu / Steven D Miller / Grigore D Pintilie / J Du Bois / Ron O Dror / Wah Chiu / Merritt Maduke / ![]() Abstract: CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different tissues. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated ...CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different tissues. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated by hyperpolarization, rather than depolarization, of the plasma membrane. The molecular basis for the divergence in polarity of voltage gating among closely related homologs has been a long-standing mystery, in part because few CLC channel structures are available. Here, we report cryoEM structures of human CLC-2 at 2.46 - 2.76 Å, in the presence and absence of the selective inhibitor AK-42. AK-42 binds within the extracellular entryway of the Cl-permeation pathway, occupying a pocket previously proposed through computational docking studies. In the apo structure, we observed two distinct conformations involving rotation of one of the cytoplasmic C-terminal domains (CTDs). In the absence of CTD rotation, an intracellular N-terminal 15-residue hairpin peptide nestles against the TM domain to physically occlude the Cl-permeation pathway. This peptide is highly conserved among species variants of CLC-2 but is not present in other CLC homologs. Previous studies suggested that the N-terminal domain of CLC-2 influences channel properties via a "ball-and-chain" gating mechanism, but conflicting data cast doubt on such a mechanism, and thus the structure of the N-terminal domain and its interaction with the channel has been uncertain. Through electrophysiological studies of an N-terminal deletion mutant lacking the 15-residue hairpin peptide, we support a model in which the N-terminal hairpin of CLC-2 stabilizes a closed state of the channel by blocking the cytoplasmic Cl-permeation pathway. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.4 KB 18.4 KB | Display Display | ![]() |
Images | ![]() | 122.8 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() | 59.3 MB 59.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ta3MC ![]() 8ta2C ![]() 8ta4C ![]() 8ta5C ![]() 8ta6C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.946 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
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Projections & Slices |
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
-Entire : Chloride channel protein 2
Entire | Name: Chloride channel protein 2 |
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Components |
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-Supramolecule #1: Chloride channel protein 2
Supramolecule | Name: Chloride channel protein 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Chloride channel protein 2
Macromolecule | Name: Chloride channel protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 95.487641 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 QEGPPSPEAS VCFQVNTEDS AFPAARGETH KPLKPALKRG PSVTRNLGES PTGSAESA G IALRSLFCGS PPPEAASEKL ESCEKRKLKR VRISLASDAD LEGEMSPEEI LEWEEQQLDE PVNFSDCKID PAPFQLVER TSLHKLRKAI EGSVTAQGVK VRPPLASFRD SATSSSDTET TEVHALWGPH SRHGLPREGS PSDSDDKCQ UniProtKB: Chloride channel protein 2 |
-Macromolecule #2: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 14300 / Average exposure time: 5.6 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: SwissModel / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Q-score |
Output model | ![]() PDB-8ta3: |