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- EMDB-30438: Structure of the human CLCN7-OSTM1 complex with ADP -

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Basic information

Entry
Database: EMDB / ID: EMD-30438
TitleStructure of the human CLCN7-OSTM1 complex with ADP
Map data
Sample
  • Complex: human CLCN7-OSTM1 complex with ADP
    • Protein or peptide: Osteopetrosis-associated transmembrane protein 1
    • Protein or peptide: H(+)/Cl(-) exchange transporter 7
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: CHLORIDE ION
KeywordsComplex / Chloride channel / lysosome / 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: 3.55 Å
AuthorsYang GH / Lu YM
CitationJournal: To Be Published
Title: Structure of the human CLCN7-OSTM1 complex with ADP
Authors: Yang GH / Lu YM / Zhang YM / Jia YT / Li XM / Lei JL
History
DepositionAug 8, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0357
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0357
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7cq7
  • Surface level: 0.0357
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30438.png

Downloads & links

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Map

FileDownload / File: emd_30438.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.)
1.1 Å/pix.
x 280 pix.
= 307.412 Å		1.1 Å/pix.
x 280 pix.
= 307.412 Å		1.1 Å/pix.
x 280 pix.
= 307.412 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0357 / Movie #1: 0.0357
Minimum - Maximum-0.06692777 - 0.11655706
Average (Standard dev.)0.00024257781 (±0.0046708398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 307.41202 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.09791.09791.0979
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z307.412307.412307.412
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0670.1170.000

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Supplemental data

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Additional map: #1

Fileemd_30438_additional_1.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 : human CLCN7-OSTM1 complex with ADP

EntireName: human CLCN7-OSTM1 complex with ADP
Components
  • Complex: human CLCN7-OSTM1 complex with ADP
    • Protein or peptide: Osteopetrosis-associated transmembrane protein 1
    • Protein or peptide: H(+)/Cl(-) exchange transporter 7
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: CHLORIDE ION

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Supramolecule #1: human CLCN7-OSTM1 complex with ADP

SupramoleculeName: human CLCN7-OSTM1 complex with ADP / 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: 38.638 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 ANIQENSNLE HHHHHHHH

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: 90.906008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASDYKDDDD KASDEVDAGT MANVSKKVSW SGRDRDDEEA APLLRRTARP GGGTPLLNGA GPGAARQSPR SALFRVGHMS SVELDDELL DPDMDPPHPF PKEIPHNEKL LSLKYESLDY DNSENQLFLE EERRINHTAF RTVEIKRWVI CALIGILTGL V ACFIDIVV ...String:
MASDYKDDDD KASDEVDAGT MANVSKKVSW SGRDRDDEEA APLLRRTARP GGGTPLLNGA GPGAARQSPR SALFRVGHMS SVELDDELL DPDMDPPHPF PKEIPHNEKL LSLKYESLDY DNSENQLFLE EERRINHTAF RTVEIKRWVI CALIGILTGL V ACFIDIVV ENLAGLKYRV IKGNIDKFTE KGGLSFSLLL WATLNAAFVL VGSVIVAFIE PVAAGSGIPQ IKCFLNGVKI PH VVRLKTL VIKVSGVILS VVGGLAVGKE GPMIHSGSVI AAGISQGRST SLKRDFKIFE YFRRDTEKRD FVSAGAAAGV SAA FGAPVG GVLFSLEEGA SFWNQFLTWR IFFASMISTF TLNFVLSIYH GNMWDLSSPG LINFGRFDSE KMAYTIHEIP VFIA MGVVG GVLGAVFNAL NYWLTMFRIR YIHRPCLQVI EAVLVAAVTA TVAFVLIYSS RDCQPLQGGS MSYPLQLFCA DGEYN SMAA AFFNTPEKSV VSLFHDPPGS YNPLTLGLFT LVYFFLACWT YGLTVSAGVF IPSLLIGAAW GRLFGISLSY LTGAAI WAD PGKYALMGAA AQLGGIVRMT LSLTVIMMEA TSNVTYGFPI MLVLMTAKIV GDVFIEGLYD MHIQLQSVPF LHWEAPV TS HSLTAREVMS TPVTCLRRRE KVGVIVDVLS DTASNHNGFP VVEHADDTQP ARLQGLILRS QLIVLLKHKV FVERSNLG L VQRRLRLKDF RDAYPRFPPI QSIHVSQDER ECTMDLSEFM NPSPYTVPQE ASLPRVFKLF RALGLRHLVV VDNRNQVVG LVTRKDLARY RLGKRGLEEL SLAQT

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

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #5: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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: 7.4
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: 1.5625 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: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 249394
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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