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- EMDB-0471: Structure of the NKCC1 CTD -

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Basic information

Entry
Database: EMDB / ID: EMD-0471
TitleStructure of the NKCC1 CTD
Map dataCytosolic domain
Sample
  • Organelle or cellular component: cytosolic domain
    • Protein or peptide: Sodium-potassium-chloride cotransporter 1
Keywordsmembrane protein
Function / homology
Function and homology information


swim bladder inflation / Cation-coupled Chloride cotransporters / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / sodium ion homeostasis / ear development / ammonium transmembrane transport / ammonium channel activity / chloride ion homeostasis / potassium ion homeostasis ...swim bladder inflation / Cation-coupled Chloride cotransporters / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / sodium ion homeostasis / ear development / ammonium transmembrane transport / ammonium channel activity / chloride ion homeostasis / potassium ion homeostasis / cell volume homeostasis / inner ear morphogenesis / potassium ion import across plasma membrane / sodium ion transmembrane transport / chloride transmembrane transport / basolateral plasma membrane / apical plasma membrane / identical protein binding
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, C-terminal / Solute carrier family 12 / Amino acid permease/ SLC12A domain / SLC12A transporter family / Amino acid permease
Similarity search - Domain/homology
Solute carrier family 12 member 2 / Solute carrier family 12 member 2
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsFeng L / Liao MF
CitationJournal: Nature / Year: 2019
Title: Structure and mechanism of the cation-chloride cotransporter NKCC1.
Authors: Thomas A Chew / Benjamin J Orlando / Jinru Zhang / Naomi R Latorraca / Amy Wang / Scott A Hollingsworth / Dong-Hua Chen / Ron O Dror / Maofu Liao / Liang Feng /
Abstract: Cation-chloride cotransporters (CCCs) mediate the electroneutral transport of chloride, potassium and/or sodium across the membrane. They have critical roles in regulating cell volume, controlling ...Cation-chloride cotransporters (CCCs) mediate the electroneutral transport of chloride, potassium and/or sodium across the membrane. They have critical roles in regulating cell volume, controlling ion absorption and secretion across epithelia, and maintaining intracellular chloride homeostasis. These transporters are primary targets for some of the most commonly prescribed drugs. Here we determined the cryo-electron microscopy structure of the Na-K-Cl cotransporter NKCC1, an extensively studied member of the CCC family, from Danio rerio. The structure defines the architecture of this protein family and reveals how cytosolic and transmembrane domains are strategically positioned for communication. Structural analyses, functional characterizations and computational studies reveal the ion-translocation pathway, ion-binding sites and key residues for transport activity. These results provide insights into ion selectivity, coupling and translocation, and establish a framework for understanding the physiological functions of CCCs and interpreting disease-related mutations.
History
DepositionJan 17, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseJul 31, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0896
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0896
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6npj
  • Surface level: 0.0896
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0471.png

Downloads & links

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Map

FileDownload / File: emd_0471.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCytosolic domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 220 pix.
= 232.1 Å		1.06 Å/pix.
x 220 pix.
= 232.1 Å		1.06 Å/pix.
x 220 pix.
= 232.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0896 / Movie #1: 0.0896
Minimum - Maximum-0.23303555 - 0.37477565
Average (Standard dev.)-0.00049207074 (±0.0118514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-110-110-110
Dimensions220220220
Spacing220220220
CellA=B=C: 232.09999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0551.0551.055
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z232.100232.100232.100
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-110-110-110
NC/NR/NS220220220
D min/max/mean-0.2330.375-0.000

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Supplemental data

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Additional map: Cytosolic domain

Fileemd_0471_additional.map
AnnotationCytosolic domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cytosolic domain

EntireName: cytosolic domain
Components
  • Organelle or cellular component: cytosolic domain
    • Protein or peptide: Sodium-potassium-chloride cotransporter 1

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Supramolecule #1: cytosolic domain

SupramoleculeName: cytosolic domain / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Sodium-potassium-chloride cotransporter 1

MacromoleculeName: Sodium-potassium-chloride cotransporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 49.444598 KDa
Recombinant expressionOrganism: Autographa californica nucleopolyhedrovirus
SequenceString: WGSSTQALTY HQALTHSLQL CGVADHIKTF RPQCLVMTGA PNSRPAILHL VHAFTKNVGL MLCGHVRISS RRPNFKELNS DMLRYQRWL LNNNSKAFYT CVVAEDLRQG TQYMLQAAGL GRLRPNTLVI GFKNDWRIGD IKEVETYINL IHDAFDFQYG V VILRLREG ...String:
WGSSTQALTY HQALTHSLQL CGVADHIKTF RPQCLVMTGA PNSRPAILHL VHAFTKNVGL MLCGHVRISS RRPNFKELNS DMLRYQRWL LNNNSKAFYT CVVAEDLRQG TQYMLQAAGL GRLRPNTLVI GFKNDWRIGD IKEVETYINL IHDAFDFQYG V VILRLREG LDISHIQGQD DSSGMKDVVV SVDISKDSDG DSSKPSSKAT SVQNSPAVQK DKKSPTVPLN VADQRLLDSQ QF QQKQGKG TVDVWWLFDD GGLTLLIPYL IANKKKWKDC KIRVFIGGKI NRIDHDRRAM ATLLSKFRID FSDITVLGDI NTK PKSEGL TEFAEMIEPY KLREDDMEQE AAEKLKSEEP WRITANELEL YKAKGNRQIR LNELLKEHSS TANLIVMSMP LARK GAVSS ALYMAWLDTL SKDLPPILLV RGNHQSVLTF YS

UniProtKB: Solute carrier family 12 member 2

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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

Concentration7.9 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60997
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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