[English] 日本語
Yorodumi
- EMDB-30543: Mouse KCC2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30543
TitleMouse KCC2
Map data
Sample
  • Organelle or cellular component: mouse KCC2
    • Protein or peptide: Solute carrier family 12 member 5
Function / homology
Function and homology information


Cation-coupled Chloride cotransporters / ammonium transmembrane transport => GO:0072488 / thermosensory behavior / intracellular pH reduction / potassium:chloride symporter activity / hypotonic response / intracellular chloride ion homeostasis / response to xenobiotic stimulus => GO:0009410 / intracellular monoatomic ion homeostasis / chloride ion homeostasis ...Cation-coupled Chloride cotransporters / ammonium transmembrane transport => GO:0072488 / thermosensory behavior / intracellular pH reduction / potassium:chloride symporter activity / hypotonic response / intracellular chloride ion homeostasis / response to xenobiotic stimulus => GO:0009410 / intracellular monoatomic ion homeostasis / chloride ion homeostasis / ammonium transmembrane transporter activity / dendritic spine development / potassium ion homeostasis / cell volume homeostasis / chloride transport / chloride transmembrane transporter activity / potassium ion import across plasma membrane / plasma membrane => GO:0005886 / monoatomic ion transport / chloride transmembrane transport / dendrite membrane / dendritic shaft / learning / cell periphery / multicellular organism growth / potassium ion transport / perikaryon / chemical synaptic transmission / membrane => GO:0016020 / neuron projection / neuronal cell body / synapse / protein kinase binding / plasma membrane
Similarity search - Function
K/Cl co-transporter 2 / K/Cl co-transporter / SLC12A transporter family / SLC12A transporter, C-terminal / Solute carrier family 12 / Amino acid permease/ SLC12A domain / Amino acid permease
Similarity search - Domain/homology
Solute carrier family 12 member 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhang S / Yang M
CitationJournal: Commun Biol / Year: 2021
Title: The structural basis of function and regulation of neuronal cotransporters NKCC1 and KCC2.
Authors: Sensen Zhang / Jun Zhou / Yuebin Zhang / Tianya Liu / Perrine Friedel / Wei Zhuo / Suma Somasekharan / Kasturi Roy / Laixing Zhang / Yang Liu / Xianbin Meng / Haiteng Deng / Wenwen Zeng / ...Authors: Sensen Zhang / Jun Zhou / Yuebin Zhang / Tianya Liu / Perrine Friedel / Wei Zhuo / Suma Somasekharan / Kasturi Roy / Laixing Zhang / Yang Liu / Xianbin Meng / Haiteng Deng / Wenwen Zeng / Guohui Li / Biff Forbush / Maojun Yang /
Abstract: NKCC and KCC transporters mediate coupled transport of Na+K+Cl and K+Cl across the plasma membrane, thus regulating cell Cl concentration and cell volume and playing critical roles in transepithelial ...NKCC and KCC transporters mediate coupled transport of Na+K+Cl and K+Cl across the plasma membrane, thus regulating cell Cl concentration and cell volume and playing critical roles in transepithelial salt and water transport and in neuronal excitability. The function of these transporters has been intensively studied, but a mechanistic understanding has awaited structural studies of the transporters. Here, we present the cryo-electron microscopy (cryo-EM) structures of the two neuronal cation-chloride cotransporters human NKCC1 (SLC12A2) and mouse KCC2 (SLC12A5), along with computational analysis and functional characterization. These structures highlight essential residues in ion transport and allow us to propose mechanisms by which phosphorylation regulates transport activity.
History
DepositionSep 13, 2020-
Header (metadata) releaseApr 14, 2021-
Map releaseApr 14, 2021-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7d14
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30543.png

Downloads & links

-
Map

FileDownload / File: emd_30543.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.091 Å
Density
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.0513047 - 0.08950083
Average (Standard dev.)0.00019440474 (±0.001956037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 349.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z349.120349.120349.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0510.0900.000

-
Supplemental data

-
Sample components

-
Entire : mouse KCC2

EntireName: mouse KCC2
Components
  • Organelle or cellular component: mouse KCC2
    • Protein or peptide: Solute carrier family 12 member 5

-
Supramolecule #1: mouse KCC2

SupramoleculeName: mouse KCC2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

-
Macromolecule #1: Solute carrier family 12 member 5

MacromoleculeName: Solute carrier family 12 member 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 126.402328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSRRFTVTSL PPAASAASAD PESRRHSVAD PRRLPREDVK GDGNPKESSP FINSTDTEKG REYDGRNMAL FEEEMDTSPM VSSLLSGLA NYTNLPQGSR EHEEAENNEG GKKKPVQAPR MGTFMGVYLP CLQNIFGVIL FLRLTWVVGI AGIMESFCMV F ICCSCTML ...String:
MSRRFTVTSL PPAASAASAD PESRRHSVAD PRRLPREDVK GDGNPKESSP FINSTDTEKG REYDGRNMAL FEEEMDTSPM VSSLLSGLA NYTNLPQGSR EHEEAENNEG GKKKPVQAPR MGTFMGVYLP CLQNIFGVIL FLRLTWVVGI AGIMESFCMV F ICCSCTML TAISMSAIAT NGVVPAGGSY YMISRSLGPE FGGAVGLCFY LGTTFAGAMY ILGTIEILLA YLFPAMAIFK AE DASGEAA AMLNNMRVYG TCVLTCMATV VFVGVKYVNK FALVFLGCVI LSILAIYAGV IKSAFDPPNF PICLLGNRTL SRH GFDVCA KLAWEGNETV TTRLWGLFCS SRLLNATCDE YFTRNNVTEI QGIPGAASGL IKENLWSSYL TKGVIVERRG MPSV GLADG TPVDMDHPYV FSDMTSYFTL LVGIYFPSVT GIMAGSNRSG DLRDAQKSIP TGTILAIATT SAVYISSVVL FGACI EGVV LRDKFGEAVN GNLVVGTLAW PSPWVIVIGS FFSTCGAGLQ SLTGAPRLLQ AISRDGIVPF LQVFGHGKAN GEPTWA LLL TACICEIGIL IASLDEVAPI LSMFFLMCYM FVNLACAVQT LLRTPNWRPR FRYYHWTLSF LGMSLCLALM FICSWYY AL VAMLIAGLIY KYIEYRGAEK EWGDGIRGLS LSAARYALLR LEEGPPHTKN WRPQLLVLVR VDQDQNVVHP QLLSLTSQ L KAGKGLTIVG SVLEGTFLDN HPQAQRAEES IRRLMEAEKV KGFCQVVISS NLRDGVSHLI QSGGLGGLQH NTVLVGWPR NWRQKEDHQT WRNFIELVRE TTAGHLALLV TKNVSMFPGN PERFSEGSID VWWIVHDGGM LMLLPFLLRH HKVWRKCKMR IFTVAQMDD NSIQMKKDLT TFLYHLRITA EVEVVEMHES DISAYTYEKT LVMEQRSQIL KQMHLTKNER EREIQSITDE S RGSIRRKN PANPRLRLNV PEETACDNEE KPEEEVQLIH DQSAPSCPSS SPSPGEEPEG ERETDPEVHL TWTKDKSVAE KN KGPSPVS SEGIKDFFSM KPEWENLNQS NVRRMHTAVR LNEVIVNKSR DAKLVLLNMP GPPRNRNGDE NYMEFLEVLT EQL DRVMLV RGGGREVITI YS

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66000

+
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