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- EMDB-7545: Human CLC-1 chloride ion channel, C-terminal cytosolic domain -

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Basic information

Entry
Database: EMDB / ID: EMD-7545
TitleHuman CLC-1 chloride ion channel, C-terminal cytosolic domain
Map dataHuman CLC-1 chloride ion channel, C-terminal cytosolic domain
Sample
  • Complex: Human CLC-1 chloride ion channel
    • Protein or peptide: Chloride channel protein 1
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 / chloride transmembrane transport / muscle contraction / sarcolemma / 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: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6coz
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
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Supplemental images

emd_7545.png

Downloads & links

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Map

FileDownload / File: emd_7545.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman CLC-1 chloride ion channel, C-terminal cytosolic domain
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.01700593 - 0.03352739
Average (Standard dev.)0.000013377495 (±0.0004063689)
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-0.0170.0340.000

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Supplemental data

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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

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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: all
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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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 39.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 175613

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6coz:
Human CLC-1 chloride ion channel, C-terminal cytosolic domain

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