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- EMDB-7544: Human CLC-1 chloride ion channel, transmembrane domain -

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Basic information

Entry
Database: EMDB / ID: EMD-7544
TitleHuman CLC-1 chloride ion channel, transmembrane domain
Map dataSummed map, filtered and sharpened
Sample
  • Complex: Human CLC-1 chloride ion channel
    • Protein or peptide: Chloride channel protein 1
  • Ligand: CHLORIDE ION
Keywordschloride / channel / CLC / TRANSPORT 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: 3.36 Å
AuthorsPark E / MacKinnon R
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2018
Title: Structure of the CLC-1 chloride channel from .
Authors: Eunyong Park / Roderick MacKinnon /
Abstract: CLC channels mediate passive Cl conduction, while CLC transporters mediate active Cl transport coupled to H transport in the opposite direction. The distinction between CLC-0/1/2 channels and CLC ...CLC channels mediate passive Cl conduction, while CLC transporters mediate active Cl transport coupled to H transport in the opposite direction. The distinction between CLC-0/1/2 channels and CLC transporters seems undetectable by amino acid sequence. To understand why they are different functionally we determined the structure of the human CLC-1 channel. Its 'glutamate gate' residue, known to mediate proton transfer in CLC transporters, adopts a location in the structure that appears to preclude it from its transport function. Furthermore, smaller side chains produce a wider pore near the intracellular surface, potentially reducing a kinetic barrier for Cl conduction. When the corresponding residues are mutated in a transporter, it is converted to a channel. Finally, Cl at key sites in the pore appear to interact with reduced affinity compared to transporters. Thus, subtle differences in glutamate gate conformation, internal pore diameter and Cl affinity distinguish CLC channels and transporters.
History
DepositionMar 13, 2018-
Header (metadata) releaseApr 25, 2018-
Map releaseJun 13, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6coy
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7544.png

Downloads & links

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Map

FileDownload / File: emd_7544.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSummed map, filtered and sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.088259995 - 0.12055682
Average (Standard dev.)0.00001340129 (±0.0026623525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.600329.600329.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0880.1210.000

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Supplemental data

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Half map: Half map 1, unfiltered

Fileemd_7544_half_map_1.map
AnnotationHalf map 1, unfiltered
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2, unfiltered

Fileemd_7544_half_map_2.map
AnnotationHalf map 2, unfiltered
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 CLC-1 chloride ion channel

EntireName: Human CLC-1 chloride ion channel
Components
  • Complex: Human CLC-1 chloride ion channel
    • Protein or peptide: Chloride channel protein 1
  • Ligand: CHLORIDE ION

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Supramolecule #1: Human CLC-1 chloride ion channel

SupramoleculeName: Human CLC-1 chloride ion 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: 108.733172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEQSRSQQRG GEQSWWGSDP QYQYMPFEHC TSYGLPSENG GLQHRLRKDA GPRHNVHPTQ IYGHHKEQFS DREQDIGMPK KTGSSSTVD SKDEDHYSKC QDCIHRLGQV VRRKLGEDGI FLVLLGLLMA LVSWSMDYVS AKSLQAYKWS YAQMQPSLPL Q FLVWVTFP ...String:
MEQSRSQQRG GEQSWWGSDP QYQYMPFEHC TSYGLPSENG GLQHRLRKDA GPRHNVHPTQ IYGHHKEQFS DREQDIGMPK KTGSSSTVD SKDEDHYSKC QDCIHRLGQV VRRKLGEDGI FLVLLGLLMA LVSWSMDYVS 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: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 4 / 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: 7.5
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: 39.0 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: EMDB MAP
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 175613
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6coy:
Human CLC-1 chloride ion channel, transmembrane domain

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