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- EMDB-30238: CLC-7/Ostm1 membrane protein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30238
TitleCLC-7/Ostm1 membrane protein complex
Map data
Sample
  • Complex: lysosomal membrane protein complex
    • Protein or peptide: Osteopetrosis-associated transmembrane protein 1
    • Protein or peptide: H(+)/Cl(-) exchange transporter 7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscomplex / lysosome / transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


transepithelial chloride transport / voltage-gated chloride channel activity / antiporter activity / chloride transmembrane transporter activity / chloride channel activity / chloride channel complex / osteoclast differentiation / Stimuli-sensing channels / lysosomal membrane / intracellular membrane-bounded organelle ...transepithelial chloride transport / voltage-gated chloride channel activity / antiporter activity / 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: 3.7 Å
AuthorsZhang SS / Yang MJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21532004, 31570733 China
CitationJournal: Sci Adv / Year: 2020
Title: Molecular insights into the human CLC-7/Ostm1 transporter.
Authors: Sensen Zhang / Yang Liu / Bing Zhang / Jun Zhou / Tianyu Li / Zhiqiang Liu / Yang Li / Maojun Yang /
Abstract: CLC family proteins translocate chloride ions across cell membranes to maintain the membrane potential, regulate the transepithelial Cl transport, and control the intravesicular pH among different ...CLC family proteins translocate chloride ions across cell membranes to maintain the membrane potential, regulate the transepithelial Cl transport, and control the intravesicular pH among different organelles. CLC-7/Ostm1 is an electrogenic Cl/H antiporter that mainly resides in lysosomes and osteoclast ruffled membranes. Mutations in human CLC-7/Ostm1 lead to lysosomal storage disorders and severe osteopetrosis. Here, we present the cryo-electron microscopy (cryo-EM) structure of the human CLC-7/Ostm1 complex and reveal that the highly glycosylated Ostm1 functions like a lid positioned above CLC-7 and interacts extensively with CLC-7 within the membrane. Our complex structure reveals a functionally crucial domain interface between the amino terminus, TMD, and CBS domains of CLC-7. Structural analyses and electrophysiology studies suggest that the domain interaction interfaces affect the slow gating kinetics of CLC-7/Ostm1. Thus, our study deepens understanding of CLC-7/Ostm1 transporter and provides insights into the molecular basis of the disease-related mutations.
History
DepositionApr 20, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bxu
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30238.png

Downloads & links

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Map

FileDownload / File: emd_30238.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.09135784 - 0.1731268
Average (Standard dev.)0.0011256913 (±0.006626737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 216.00002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z216.000216.000216.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0910.1730.001

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Supplemental data

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Sample components

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Entire : lysosomal membrane protein complex

EntireName: lysosomal membrane protein complex
Components
  • Complex: lysosomal membrane protein complex
    • Protein or peptide: Osteopetrosis-associated transmembrane protein 1
    • Protein or peptide: H(+)/Cl(-) exchange transporter 7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: lysosomal membrane protein complex

SupramoleculeName: lysosomal membrane protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Osteopetrosis-associated transmembrane protein 1

MacromoleculeName: Osteopetrosis-associated transmembrane protein 1 / type: protein_or_peptide / ID: 1 / 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 #2: H(+)/Cl(-) exchange transporter 7

MacromoleculeName: H(+)/Cl(-) exchange transporter 7 / type: protein_or_peptide / ID: 2 / 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 #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 14 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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 K2 SUMMIT (4k 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3956
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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