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- EMDB-37909: human CLC-1 D136G closed state -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-37909
Titlehuman CLC-1 D136G closed state
Map data
Sample
  • Complex: CLC-1 channel
    • Protein or peptide: Chloride channel protein 1
  • Ligand: THIOCYANATE ION
KeywordsChannel / MEMBRANE PROTEIN
Function / homology
Function and homology information


voltage-gated chloride channel activity / neuronal action potential propagation / chloride transport / chloride channel complex / T-tubule / muscle contraction / chloride transmembrane transport / Stimuli-sensing channels / protein homodimerization activity / plasma membrane
Similarity search - Function
Chloride channel ClC-1 / : / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / CBS domain superfamily / CBS domain profile.
Similarity search - Domain/homology
Chloride channel protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsZhang MF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CLC-1 in SCN environment
Authors: Zhang MF
History
DepositionOct 29, 2023-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37909.png

Downloads & links

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Map

FileDownload / File: emd_37909.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.35 Å/pix.
x 720 pix.
= 252. Å		0.35 Å/pix.
x 720 pix.
= 252. Å		0.35 Å/pix.
x 720 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.12743711 - 0.21191408
Average (Standard dev.)0.000026938098 (±0.005806693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 252.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37909_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37909_half_map_2.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 : CLC-1 channel

EntireName: CLC-1 channel
Components
  • Complex: CLC-1 channel
    • Protein or peptide: Chloride channel protein 1
  • Ligand: THIOCYANATE ION

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Supramolecule #1: CLC-1 channel

SupramoleculeName: CLC-1 channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Chloride channel protein 1

MacromoleculeName: Chloride channel protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 108.675133 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEQSRSQQRG GEQSWWGSDP QYQYMPFEHC TSYGLPSENG GLQHRLRKDA GPRHNVHPTQ IYGHHKEQFS DREQDIGMPK KTGSSSTVD SKDEDHYSKC QDCIHRLGQV VRRKLGEDGI FLVLLGLLMA LVSWSMGYVS AKSLQAYKWS YAQMQPSLPL Q FLVWVTFP ...String:
MEQSRSQQRG GEQSWWGSDP QYQYMPFEHC TSYGLPSENG GLQHRLRKDA GPRHNVHPTQ IYGHHKEQFS DREQDIGMPK KTGSSSTVD SKDEDHYSKC QDCIHRLGQV VRRKLGEDGI FLVLLGLLMA LVSWSMGYVS AKSLQAYKWS YAQMQPSLPL Q FLVWVTFP LVLILFSALF CHLISPQAVG SGIPEMKTIL RGVVLKEYLT MKAFVAKVVA LTAGLGSGIP VGKEGPFVHI AS ICAAVLS KFMSVFCGVY EQPYYYSDIL TVGCAVGVGC CFGTPLGGVL FSIEVTSTYF AVRNYWRGFF AATFSAFVFR VLA VWNKDA VTITALFRTN FRMDFPFDLK ELPAFAAIGI CCGLLGAVFV YLHRQVMLGV RKHKALSQFL AKHRLLYPGI VTFV IASFT FPPGMGQFMA GELMPREAIS TLFDNNTWVK HAGDPESLGQ SAVWIHPRVN VVIIIFLFFV MKFWMSIVAT TMPIP CGGF MPVFVLGAAF GRLVGEIMAM LFPDGILFDD IIYKILPGGY AVIGAAALTG AVSHTVSTAV ICFELTGQIA HILPMM VAV ILANMVAQSL QPSLYDSIIQ VKKLPYLPDL GWNQLSKYTI FVEDIMVRDV KFVSASYTYG ELRTLLQTTT VKTLPLV DS KDSMILLGSV ERSELQALLQ RHLCPERRLR AAQEMARKLS ELPYDGKARL AGEGLPGAPP GRPESFAFVD EDEDEDLS G KSELPPSLAL HPSTTAPLSP EEPNGPLPGH KQQPEAPEPA GQRPSIFQSL LHCLLGRARP TKKKTTQDST DLVDNMSPE EIEAWEQEQL SQPVCFDSCC IDQSPFQLVE QTTLHKTHTL FSLLGLHLAY VTSMGKLRGV LALEELQKAI EGHTKSGVQL RPPLASFRN TTSTRKSTGA PPSSAENWNL PEDRPGATGT GDVIAASPET PVPSPSPEPP LSLAPGKVEG ELEELELVES P GLEEELAD ILQGPSLRST DEEDEDELIL

UniProtKB: Chloride channel protein 1

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Macromolecule #2: THIOCYANATE ION

MacromoleculeName: THIOCYANATE ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: SCN
Molecular weightTheoretical: 58.082 Da
Chemical component information

ChemComp-SCN:
THIOCYANATE ION

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36886
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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