[English] 日本語
Yorodumi
- EMDB-37908: human CLC-1 D136G delayed rectification -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37908
Titlehuman CLC-1 D136G delayed rectification
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 / muscle contraction / T-tubule / 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: 2.57 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 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37908.png

Downloads & links

-
Map

FileDownload / File: emd_37908.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-0.14100467 - 0.2514919
Average (Standard dev.)0.00002206664 (±0.00650159)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_37908_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37908_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CLC-1 channel

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

-
Supramolecule #1: CLC-1 channel

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

-
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

-
Macromolecule #2: THIOCYANATE ION

MacromoleculeName: THIOCYANATE ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: SCN
Molecular weightTheoretical: 58.082 Da
Chemical component information

ChemComp-SCN:
THIOCYANATE ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38321
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more