[English] 日本語
Yorodumi
- EMDB-30542: Human NKCC1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30542
TitleHuman NKCC1Na-K-Cl cotransporter
Map data
Sample
  • Complex: human NKCC1Na-K-Cl cotransporter
    • Protein or peptide: Solute carrier family 12 member 2
  • Ligand: PALMITIC ACID
Function / homology
Function and homology information


positive regulation of cell volume / positive regulation of aspartate secretion / transepithelial ammonium transport / regulation of matrix metallopeptidase secretion / cell body membrane / inorganic anion import across plasma membrane / inorganic cation import across plasma membrane / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / metal ion transmembrane transporter activity ...positive regulation of cell volume / positive regulation of aspartate secretion / transepithelial ammonium transport / regulation of matrix metallopeptidase secretion / cell body membrane / inorganic anion import across plasma membrane / inorganic cation import across plasma membrane / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / metal ion transmembrane transporter activity / transepithelial chloride transport / potassium ion transmembrane transporter activity / Cation-coupled Chloride cotransporters / ammonium transmembrane transport / sodium ion homeostasis / intracellular chloride ion homeostasis / negative regulation of vascular wound healing / chloride ion homeostasis / cellular response to potassium ion / ammonium channel activity / intracellular potassium ion homeostasis / cell projection membrane / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / potassium ion homeostasis / cellular response to chemokine / T cell chemotaxis / hyperosmotic response / gamma-aminobutyric acid signaling pathway / cell volume homeostasis / regulation of spontaneous synaptic transmission / maintenance of blood-brain barrier / potassium ion import across plasma membrane / transport across blood-brain barrier / sodium ion transmembrane transport / lateral plasma membrane / monoatomic ion transport / chloride transmembrane transport / basal plasma membrane / cell projection / cell periphery / Hsp90 protein binding / cytoplasmic vesicle membrane / extracellular vesicle / cell body / protein-folding chaperone binding / basolateral plasma membrane / neuron projection / apical plasma membrane / neuronal cell body / protein kinase binding / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Solute carrier family 12 member 1/2 / Solute carrier family 12 member 2 / Amino acid permease, N-terminal / Amino acid permease N-terminal / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 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 12, 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: 0.058
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.058
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7d10
  • Surface level: 0.058
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30542.png

Downloads & links

-
Map

FileDownload / File: emd_30542.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.091 Å
Density
Contour LevelBy AUTHOR: 0.058 / Movie #1: 0.058
Minimum - Maximum-0.17495783 - 0.30946833
Average (Standard dev.)0.0014723054 (±0.009292715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 218.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z218.200218.200218.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1750.3090.001

-
Supplemental data

-
Sample components

-
Entire : human NKCC1

EntireName: human NKCC1Na-K-Cl cotransporter
Components
  • Complex: human NKCC1Na-K-Cl cotransporter
    • Protein or peptide: Solute carrier family 12 member 2
  • Ligand: PALMITIC ACID

-
Supramolecule #1: human NKCC1

SupramoleculeName: human NKCC1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

-
Macromolecule #1: Solute carrier family 12 member 2

MacromoleculeName: Solute carrier family 12 member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 131.583422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEPRPTAPSS GAPGLAGVGE TPSAAALAAA RVELPGTAVP SVPEDAAPAS RDGGGVRDEG PAAAGDGLGR PLGPTPSQSR FQVDLVSEN AGRAAAAAAA AAAAAAAAGA GAGAKQTPAD GEASGESEPA KGSEEAKGRF RVNFVDPAAS SSAEDSLSDA A GVGVDGPN ...String:
MEPRPTAPSS GAPGLAGVGE TPSAAALAAA RVELPGTAVP SVPEDAAPAS RDGGGVRDEG PAAAGDGLGR PLGPTPSQSR FQVDLVSEN AGRAAAAAAA AAAAAAAAGA GAGAKQTPAD GEASGESEPA KGSEEAKGRF RVNFVDPAAS SSAEDSLSDA A GVGVDGPN VSFQNGGDTV LSEGSSLHSG GGGGSGHHQH YYYDTHTNTY YLRTFGHNTM DAVPRIDHYR HTAAQLGEKL LR PSLAELH DELEKEPFED GFANGEESTP TRDAVVTYTA ESKGVVKFGW IKGVLVRCML NIWGVMLFIR LSWIVGQAGI GLS VLVIMM ATVVTTITGL STSAIATNGF VRGGGAYYLI SRSLGPEFGG AIGLIFAFAN AVAVAMYVVG FAETVVELLK EHSI LMIDE INDIRIIGAI TVVILLGISV AGMEWEAKAQ IVLLVILLLA IGDFVIGTFI PLESKKPKGF FGYKSEIFNE NFGPD FREE ETFFSVFAIF FPAATGILAG ANISGDLADP QSAIPKGTLL AILITTLVYV GIAVSVGSCV VRDATGNVND TIVTEL TNC TSAACKLNFD FSSCESSPCS YGLMNNFQVM SMVSGFTPLI SAGIFSATLS SALASLVSAP KIFQALCKDN IYPAFQM FA KGYGKNNEPL RGYILTFLIA LGFILIAELN VIAPIISNFF LASYALINFS VFHASLAKSP GWRPAFKYYN MWISLLGA I LCCIVMFVIN WWAALLTYVI VLGLYIYVTY KKPDVNWGSS TQALTYLNAL QHSIRLSGVE DHVKNFRPQC LVMTGAPNS RPALLHLVHD FTKNVGLMIC GHVHMGPRRQ AMKEMSIDQA KYQRWLIKNK MKAFYAPVHA DDLREGAQYL MQAAGLGRMK PNTLVLGFK KDWLQADMRD VDMYINLFHD AFDIQYGVVV IRLKEGLDIS HLQGQEELLS SQEKSPGTKD VVVSVEYSKK S DLDTSKPL SEKPITHKVE EEDGKTATQP LLKKESKGPI VPLNVADQKL LEASTQFQKK QGKNTIDVWW LFDDGGLTLL IP YLLTTKK KWKDCKIRVF IGGKINRIDH DRRAMATLLS KFRIDFSDIM VLGDINTKPK KENIIAFEEI IEPYRLHEDD KEQ DIADKM KEDEPWRITD NELELYKTKT YRQIRLNELL KEHSSTANII VMSLPVARKG AVSSALYMAW LEALSKDLPP ILLV RGNHQ SVLTFYS

-
Macromolecule #2: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 2 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

-
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: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80000

+
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