[English] 日本語
Yorodumi
- EMDB-30616: human potassium-chloride co-transporter KCC3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30616
Titlehuman potassium-chloride co-transporter KCC3
Map data
Sample
  • Complex: potassium-chloride cotransporter 3
    • Protein or peptide: potassium-chloride cotransporter 3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordspotassium-chloride / co-transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / potassium ion transmembrane transporter activity / chloride ion homeostasis / cellular hypotonic salinity response / cellular hypotonic response / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane ...Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / potassium ion transmembrane transporter activity / chloride ion homeostasis / cellular hypotonic salinity response / cellular hypotonic response / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / monoatomic ion transport / potassium ion transmembrane transport / chloride transmembrane transport / cellular response to glucose stimulus / angiogenesis / basolateral plasma membrane / chemical synaptic transmission / axon / synapse / protein kinase binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
K/Cl co-transporter / SLC12A transporter, C-terminal / Solute carrier family 12 / SLC12A transporter family / Amino acid permease/ SLC12A domain / Amino acid permease
Similarity search - Domain/homology
Solute carrier family 12 member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsXie Y / Chang S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870724 China
CitationJournal: Sci Adv / Year: 2020
Title: Structures and an activation mechanism of human potassium-chloride cotransporters.
Authors: Yuan Xie / Shenghai Chang / Cheng Zhao / Feng Wang / Si Liu / Jin Wang / Eric Delpire / Sheng Ye / Jiangtao Guo /
Abstract: Potassium-chloride cotransporters KCC1 to KCC4 mediate the coupled export of potassium and chloride across the plasma membrane and play important roles in cell volume regulation, auditory system ...Potassium-chloride cotransporters KCC1 to KCC4 mediate the coupled export of potassium and chloride across the plasma membrane and play important roles in cell volume regulation, auditory system function, and γ-aminobutyric acid (GABA) and glycine-mediated inhibitory neurotransmission. Here, we present 2.9- to 3.6-Å resolution structures of full-length human KCC2, KCC3, and KCC4. All three KCCs adopt a similar overall architecture, a domain-swap dimeric assembly, and an inward-facing conformation. The structural and functional studies reveal that one unexpected N-terminal peptide binds at the cytosolic facing cavity and locks KCC2 and KCC4 at an autoinhibition state. The C-terminal domain (CTD) directly interacts with the N-terminal inhibitory peptide, and the relative motions between the CTD and the transmembrane domain (TMD) suggest that CTD regulates KCCs' activities by adjusting the autoinhibitory effect. These structures provide the first glimpse of full-length structures of KCCs and an autoinhibition mechanism among the amino acid-polyamine-organocation transporter superfamily.
History
DepositionOct 12, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7d90
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30616.png

Downloads & links

-
Map

FileDownload / File: emd_30616.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.022600185 - 0.05080551
Average (Standard dev.)-0.000045897854 (±0.0025808385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 243.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z243.360243.360243.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0230.051-0.000

-
Supplemental data

-
Sample components

-
Entire : potassium-chloride cotransporter 3

EntireName: potassium-chloride cotransporter 3
Components
  • Complex: potassium-chloride cotransporter 3
    • Protein or peptide: potassium-chloride cotransporter 3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: potassium-chloride cotransporter 3

SupramoleculeName: potassium-chloride cotransporter 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: potassium-chloride cotransporter 3

MacromoleculeName: potassium-chloride cotransporter 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.920758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKM HPPETTTKMA SVRFMVTPTK IDDIPGLSDT SPDLSSRSSS RVRFSSRESV PETSRSEPMS EMSGATTSLA TVALDPPSD RTSHPQDVIE DLSQNSITGE HSQLLDDGHK KARNAYLNNS NYEEGDEYFD KNLALFEEEM DTRPKVSSLL N RMANYTNL ...String:
MDYKDDDDKM HPPETTTKMA SVRFMVTPTK IDDIPGLSDT SPDLSSRSSS RVRFSSRESV PETSRSEPMS EMSGATTSLA TVALDPPSD RTSHPQDVIE DLSQNSITGE HSQLLDDGHK KARNAYLNNS NYEEGDEYFD KNLALFEEEM DTRPKVSSLL N RMANYTNL TQGAKEHEEA ENITEGKKKP TKTPQMGTFM GVYLPCLQNI FGVILFLRLT WVVGTAGVLQ AFAIVLICCC CT MLTAISM SAIATNGVVP AGGSYFMISR ALGPEFGGAV GLCFYLGTTF AAAMYILGAI EIFLVYIVPR AAIFHSDDAL KES AAMLNN MRVYGTAFLV LMVLVVFIGV RYVNKFASLF LACVIVSILA IYAGAIKSSF APPHFPVCML GNRTLSSRHI DVCS KTKEI NNMTVPSKLW GFFCNSSQFF NATCDEYFVH NNVTSIQGIP GLASGIITEN LWSNYLPKGE IIEKPSAKSS DVLGS LNHE YVLVDITTSF TLLVGIFFPS VTGIMAGSNR SGDLKDAQKS IPIGTILAIL TTSFVYLSNV VLFGACIEGV VLRDKF GDA VKGNLVVGTL SWPSPWVIVI GSFFSTCGAG LQSLTGAPRL LQAIAKDNII PFLRVFGHSK ANGEPTWALL LTAAIAE LG ILIASLDLVA PILSMFFLMC YLFVNLACAL QTLLRTPNWR PRFRYYHWAL SFMGMSICLA LMFISSWYYA IVAMVIAG M IYKYIEYQGA EKEWGDGIRG LSLSAARFAL LRLEEGPPHT KNWRPQLLVL LKLDEDLHVK HPRLLTFASQ LKAGKGLTI VGSVIVGNFL ENYGEALAAE QTIKHLMEAE KVKGFCQLVV AAKLREGISH LIQSCGLGGM KHNTVVMGWP NGWRQSEDAR AWKTFIGTV RVTTAAHLAL LVAKNISFFP SNVEQFSEGN IDVWWIVHDG GMLMLLPFLL KQHKVWRKCS IRIFTVAQLE D NSIQMKKD LATFLYHLRI EAEVEVVEMH DSDISAYTYE RTLMMEQRSQ MLRHMRLSKT ERDREAQLVK DRNSMLRLTS IG SDEDEET ETYQEKVHMT WTKDKYMASR GQKAKSMEGF QDLLNMRPDQ SNVRRMHTAV KLNEVIVNKS HEAKLVLLNM PGP PRNPEG DENYMEFLEV LTEGLERVLL VRGGGSEVIT IYSWSHPQFE K

UniProtKB: Solute carrier family 12 member 6

-
Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.0 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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84675
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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