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- EMDB-51098: CLC7/OSTM1 complex in the absence of PIP2 lipid. -

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Basic information

Entry
Database: EMDB / ID: EMD-51098
TitleCLC7/OSTM1 complex in the absence of PIP2 lipid.
Map data
Sample
  • Complex: Hetero-tetrameric complex of human WT-CLC7 (Apo) with OSTM1
    • Protein or peptide: H(+)/Cl(-) exchange transporter 7
    • Protein or peptide: Osteopetrosis-associated transmembrane protein 1
  • Ligand: CHLORIDE ION
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsLysosomal transporter / pH Regulation / Membrane Complex / Transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


transepithelial chloride transport / chloride:proton antiporter activity / response to pH / chloride transmembrane transporter activity / chloride channel activity / chloride channel complex / osteoclast differentiation / Stimuli-sensing channels / lysosomal membrane / intracellular membrane-bounded organelle ...transepithelial chloride transport / chloride:proton antiporter activity / response to pH / chloride transmembrane transporter activity / chloride channel activity / chloride channel complex / osteoclast differentiation / Stimuli-sensing channels / lysosomal membrane / intracellular membrane-bounded organelle / ATP binding / membrane / cytosol
Similarity search - Function
Osteopetrosis-associated transmembrane protein 1 precursor / Osteopetrosis-associated transmembrane protein 1 precursor / 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 superfamily / CBS domain ...Osteopetrosis-associated transmembrane protein 1 precursor / Osteopetrosis-associated transmembrane protein 1 precursor / 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 superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
H(+)/Cl(-) exchange transporter 7 / Osteopetrosis-associated transmembrane protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLin Y / Deme JC / Lea SM / Newstead S
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Mechanism of phosphoinositide regulation of lysosomal pH via inhibition of CLC7
Authors: Hilton J / Lin Y / Sefah E / Deme JC / Parker J / Langton MJ / Grabe M / Lea S / Newstead S / Mindell JA
History
DepositionJul 18, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51098.png

Downloads & links

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Map

FileDownload / File: emd_51098.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 512 pix.
= 354.816 Å		0.69 Å/pix.
x 512 pix.
= 354.816 Å		0.69 Å/pix.
x 512 pix.
= 354.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.693 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.5274369 - 1.0780584
Average (Standard dev.)-0.0007745045 (±0.020643465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 354.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51098_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Mask #2

Fileemd_51098_msk_2.map
Projections & Slices
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Additional map: #1

Fileemd_51098_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_51098_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_51098_half_map_2.map
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Sample components

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Entire : Hetero-tetrameric complex of human WT-CLC7 (Apo) with OSTM1

EntireName: Hetero-tetrameric complex of human WT-CLC7 (Apo) with OSTM1
Components
  • Complex: Hetero-tetrameric complex of human WT-CLC7 (Apo) with OSTM1
    • Protein or peptide: H(+)/Cl(-) exchange transporter 7
    • Protein or peptide: Osteopetrosis-associated transmembrane protein 1
  • Ligand: CHLORIDE ION
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: Hetero-tetrameric complex of human WT-CLC7 (Apo) with OSTM1

SupramoleculeName: Hetero-tetrameric complex of human WT-CLC7 (Apo) with OSTM1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: H(+)/Cl(-) exchange transporter 7

MacromoleculeName: H(+)/Cl(-) exchange transporter 7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.773875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MANVSKKVSW SGRDRDDEEA APLLRRTARP GGGTPLLNGA GPGAARQSPR SALFRVGHMS SVELDDELLD PDMDPPHPFP KEIPHNEKL LSLKYESLDY DNSENQLFLE EERRINHTAF RTVEIKRWVI CALIGILTGL VACFIDIVVE NLAGLKYRVI K GNIDKFTE ...String:
MANVSKKVSW SGRDRDDEEA APLLRRTARP GGGTPLLNGA GPGAARQSPR SALFRVGHMS SVELDDELLD PDMDPPHPFP KEIPHNEKL LSLKYESLDY DNSENQLFLE EERRINHTAF RTVEIKRWVI CALIGILTGL VACFIDIVVE NLAGLKYRVI K GNIDKFTE KGGLSFSLLL WATLNAAFVL VGSVIVAFIE PVAAGSGIPQ IKCFLNGVKI PHVVRLKTLV IKVSGVILSV VG GLAVGKE GPMIHSGSVI AAGISQGRST SLKRDFKIFE YFRRDTEKRD FVSAGAAAGV SAAFGAPVGG VLFSLEEGAS FWN QFLTWR IFFASMISTF TLNFVLSIYH GNMWDLSSPG LINFGRFDSE KMAYTIHEIP VFIAMGVVGG VLGAVFNALN YWLT MFRIR YIHRPCLQVI EAVLVAAVTA TVAFVLIYSS RDCQPLQGGS MSYPLQLFCA DGEYNSMAAA FFNTPEKSVV SLFHD PPGS YNPLTLGLFT LVYFFLACWT YGLTVSAGVF IPSLLIGAAW GRLFGISLSY LTGAAIWADP GKYALMGAAA QLGGIV RMT LSLTVIMMEA TSNVTYGFPI MLVLMTAKIV GDVFIEGLYD MHIQLQSVPF LHWEAPVTSH SLTAREVMST PVTCLRR RE KVGVIVDVLS DTASNHNGFP VVEHADDTQP ARLQGLILRS QLIVLLKHKV FVERSNLGLV QRRLRLKDFR DAYPRFPP I QSIHVSQDER ECTMDLSEFM NPSPYTVPQE ASLPRVFKLF RALGLRHLVV VDNRNQVVGL VTRKDLARYR LGKRGLEEL SLAQT

UniProtKB: H(+)/Cl(-) exchange transporter 7

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Macromolecule #2: Osteopetrosis-associated transmembrane protein 1

MacromoleculeName: Osteopetrosis-associated transmembrane protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.29057 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEPGPTAAQR RCSLPPWLPL GLLLWSGLAL GALPFGSSPH RVFHDLLSEQ QLLEVEDLSL SLLQGGGLGP LSLPPDLPDL DPECRELLL DFANSSAELT GCLVRSARPV RLCQTCYPLF QQVVSKMDNI SRAAGNTSES QSCARSLLMA DRMQIVVILS E FFNTTWQE ...String:
MEPGPTAAQR RCSLPPWLPL GLLLWSGLAL GALPFGSSPH RVFHDLLSEQ QLLEVEDLSL SLLQGGGLGP LSLPPDLPDL DPECRELLL DFANSSAELT GCLVRSARPV RLCQTCYPLF QQVVSKMDNI SRAAGNTSES QSCARSLLMA DRMQIVVILS E FFNTTWQE ANCANCLTNN SEELSNSTVY FLNLFNHTLT CFEHNLQGNA HSLLQTKNYS EVCKNCREAY KTLSSLYSEM QK MNELENK AEPGTHLCID VEDAMNITRK LWSRTFNCSV PCSDTVPVIA VSVFILFLPV VFYLSSFLHS EQKKRKLILP KRL KSSTSF ANIQENSN

UniProtKB: Osteopetrosis-associated transmembrane protein 1

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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: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 6 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.7 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: 0.5 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 210876
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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