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- EMDB-22386: Structure of chicken CLC-7 -

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Basic information

Entry
Database: EMDB / ID: EMD-22386
TitleStructure of chicken CLC-7
Map dataDensity map of chicken CLC-7
Sample
  • Complex: Chicken CLC-7
    • Protein or peptide: Chloride channel protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: CHLORIDE IONChloride
  • Ligand: (2R)-3-{[(R)-hydroxy{[(1S,2R,3S,4S,5R,6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dinonanoate
  • Ligand: water
KeywordsLysosomal / chloride-proton antiporter / chloride transport / ion transport / proton transport / MEMBRANE PROTEIN
Function / homology
Function and homology information


Stimuli-sensing channels / voltage-gated chloride channel activity / chloride transmembrane transporter activity / transmembrane transporter activity / membrane => GO:0016020 / intracellular membrane-bounded organelle / nucleoplasm
Similarity search - Function
Chloride channel ClC-7 / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
Chloride channel protein / Chloride channel protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsSchrecker M / Hite R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA008748 United States
CitationJournal: Elife / Year: 2020
Title: Cryo-EM structure of the lysosomal chloride-proton exchanger CLC-7 in complex with OSTM1.
Authors: Marina Schrecker / Julia Korobenko / Richard K Hite /
Abstract: The chloride-proton exchanger CLC-7 plays critical roles in lysosomal homeostasis and bone regeneration and its mutation can lead to osteopetrosis, lysosomal storage disease and neurological ...The chloride-proton exchanger CLC-7 plays critical roles in lysosomal homeostasis and bone regeneration and its mutation can lead to osteopetrosis, lysosomal storage disease and neurological disorders. In lysosomes and the ruffled border of osteoclasts, CLC-7 requires a β-subunit, OSTM1, for stability and activity. Here, we present electron cryomicroscopy structures of CLC-7 in occluded states by itself and in complex with OSTM1, determined at resolutions up to 2.8 Å. In the complex, the luminal surface of CLC-7 is entirely covered by a dimer of the heavily glycosylated and disulfide-bonded OSTM1, which serves to protect CLC-7 from the degradative environment of the lysosomal lumen. OSTM1 binding does not induce large-scale rearrangements of CLC-7, but does have minor effects on the conformation of the ion-conduction pathway, potentially contributing to its regulatory role. These studies provide insights into the role of OSTM1 and serve as a foundation for understanding the mechanisms of CLC-7 regulation.
History
DepositionJul 31, 2020-
Header (metadata) releaseSep 2, 2020-
Map releaseSep 2, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jm6
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22386.png

Downloads & links

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Map

FileDownload / File: emd_22386.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of chicken CLC-7
Voxel sizeX=Y=Z: 0.71487 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-15.602301000000001 - 21.485289999999999
Average (Standard dev.)0.00000000000938 (±0.4267109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 274.5088 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.71486718750.71486718750.7148671875
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z274.509274.509274.509
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-15.60221.4850.000

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Supplemental data

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Sample components

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Entire : Chicken CLC-7

EntireName: Chicken CLC-7
Components
  • Complex: Chicken CLC-7
    • Protein or peptide: Chloride channel protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: CHLORIDE IONChloride
  • Ligand: (2R)-3-{[(R)-hydroxy{[(1S,2R,3S,4S,5R,6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dinonanoate
  • Ligand: water

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Supramolecule #1: Chicken CLC-7

SupramoleculeName: Chicken CLC-7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken)

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Macromolecule #1: Chloride channel protein

MacromoleculeName: Chloride channel protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 88.684609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MANVAKKVSW SGRDPRDDED ERAGETTPLL NGTGPGSAGG ARQFTPSSFL RPGQLSNVDL NEDIRELETE LPRPYPNEIP HNEKLLSLK YESLDYDNSE NQLFLEEERR INHAAFRTVE IKRWVICAMI GILTGLVACF IDIVVENLAG LKYRVVKDNI D KFTEKGGL ...String:
MANVAKKVSW SGRDPRDDED ERAGETTPLL NGTGPGSAGG ARQFTPSSFL RPGQLSNVDL NEDIRELETE LPRPYPNEIP HNEKLLSLK YESLDYDNSE NQLFLEEERR INHAAFRTVE IKRWVICAMI GILTGLVACF IDIVVENLAG LKYRVVKDNI D KFTEKGGL SFSLLLWATL NASVVMVGSV IVAFIEPVAA GSGIPQIKCY LNGVKIPHVV RLKTLVIKVC GVILSVVGGL AV GKEGPMI HSGAVIAAGI SQGRSTSLKR DFKIFEYFRR DTEKRDFVSA GAAAGVSAAF GAPVGGVLFS LEEGASFWNQ FLT WRIFFA SMISTFTLNS VLSVYHGNAW DLSSPGLINF GRFDSEKMGY TIQEIPIFIF MGVVGGILGA LFNALNYWLT MFRI RYIHR PCLQVIEAML VAAVTAAVGF VMIYCSRDCQ PIQGSSVAYP LQLFCADGEY NSMATAFFNT PEKSVVNLFH DPPGS YNPM TLGMFTLMYF FLACWTYGLT VSAGVFIPSL LIGAAWGRLF GISLSYLSKG SIWADPGKYA LMGAAAQLGG IVRMTL SLT VIMMEATGNV TYGFPIMLVL MTAKIVGDYF VEGLYDMHIQ LQSVPFLHWE APVTSHSLTA REVMSTPVTC LRRIERV GT VVDILSDTSS NHNGFPVVES NPNTTQVAGL RGLILRSQLI VLLKHKVFVE RANLNLVQRR LKLKDFRDAY PRFPPIQS I HVSQDERECM IDLSEFMNPS PYTVPREASL PRVFKLFRAL GLRHLVVVNN HNEVVGMVTR KDLARYRLGK EGLEELSLA QT

UniProtKB: Chloride channel protein

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

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

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

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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: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #5: (2R)-3-{[(R)-hydroxy{[(1S,2R,3S,4S,5R,6R)-2,3,4,6-tetrahydroxy-5-...

MacromoleculeName: (2R)-3-{[(R)-hydroxy{[(1S,2R,3S,4S,5R,6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dinonanoate
type: ligand / ID: 5 / Number of copies: 2 / Formula: 0J1
Molecular weightTheoretical: 694.64 Da
Chemical component information

ChemComp-0J1:
(2R)-3-{[(R)-hydroxy{[(1S,2R,3S,4S,5R,6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dinonanoate

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 72 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormula
150.0 mMKCL
50.0 mMTris
2.0 mMDTT
0.01 %LMNG
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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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: OTHER / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.2 µm / Nominal magnification: 22500
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 44.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: CryoSparc Ab-initio
Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. V2.15.0)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. V2.15.0) / Details: CryoSparc Non-uniform refinement
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 87707

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7jm6:
Structure of chicken CLC-7

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