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- EMDB-29097: Cryo-EM structure of human NCC (class 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-29097
TitleCryo-EM structure of human NCC (class 1)
Map data
Sample
  • Complex: NCC-polythiazide complex
    • Protein or peptide: Solute carrier family 12 member 2,Solute carrier family 12 member 3 chimera
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: Polythiazide
  • Ligand: SODIUM ION
KeywordsMembrane transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


swim bladder inflation / Cation-coupled Chloride cotransporters / Defective SLC12A3 causes Gitelman syndrome (GS) / sodium:chloride symporter activity / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / sodium ion homeostasis / ear development / renal sodium ion absorption ...swim bladder inflation / Cation-coupled Chloride cotransporters / Defective SLC12A3 causes Gitelman syndrome (GS) / sodium:chloride symporter activity / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / sodium ion homeostasis / ear development / renal sodium ion absorption / ammonium transmembrane transport / ammonium channel activity / chloride ion homeostasis / potassium ion homeostasis / cell volume homeostasis / inner ear morphogenesis / response to aldosterone / sodium ion transport / potassium ion import across plasma membrane / response to dietary excess / sodium ion transmembrane transport / monoatomic ion transport / chloride transmembrane transport / basolateral plasma membrane / apical plasma membrane / signal transduction / extracellular exosome / ATP binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Thiazide-sensitive Na-K-Cl co-transporter / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsZhang J / Fan M / Feng L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2023
Title: Structure and thiazide inhibition mechanism of the human Na-Cl cotransporter.
Authors: Minrui Fan / Jianxiu Zhang / Chien-Ling Lee / Jinru Zhang / Liang Feng /
Abstract: The sodium-chloride cotransporter (NCC) is critical for kidney physiology. The NCC has a major role in salt reabsorption in the distal convoluted tubule of the nephron, and mutations in the NCC cause ...The sodium-chloride cotransporter (NCC) is critical for kidney physiology. The NCC has a major role in salt reabsorption in the distal convoluted tubule of the nephron, and mutations in the NCC cause the salt-wasting disease Gitelman syndrome. As a key player in salt handling, the NCC regulates blood pressure and is the target of thiazide diuretics, which have been widely prescribed as first-line medications to treat hypertension for more than 60 years. Here we determined the structures of human NCC alone and in complex with a commonly used thiazide diuretic using cryo-electron microscopy. These structures, together with functional studies, reveal major conformational states of the NCC and an intriguing regulatory mechanism. They also illuminate how thiazide diuretics specifically interact with the NCC and inhibit its transport function. Our results provide critical insights for understanding the Na-Cl cotransport mechanism of the NCC, and they establish a framework for future drug design and for interpreting disease-related mutations.
History
DepositionDec 14, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29097.png

Downloads & links

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Map

FileDownload / File: emd_29097.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.3571578 - 2.3348706
Average (Standard dev.)-0.0010613088 (±0.05717325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29097_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29097_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29097_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : NCC-polythiazide complex

EntireName: NCC-polythiazide complex
Components
  • Complex: NCC-polythiazide complex
    • Protein or peptide: Solute carrier family 12 member 2,Solute carrier family 12 member 3 chimera
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: Polythiazide
  • Ligand: SODIUM ION

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Supramolecule #1: NCC-polythiazide complex

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

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Macromolecule #1: Solute carrier family 12 member 2,Solute carrier family 12 member...

MacromoleculeName: Solute carrier family 12 member 2,Solute carrier family 12 member 3 chimera
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120.372164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSASPPISAG DYLSAPEPDA LKPAGPTPSQ SRFQVDLVTE SAGDGETTVG FDSSPPEYVA EPPPDGLRDS VSGGEKAKGR FRVVNFAAS SPDAAPAETA QNGDTVMSEG SLHSSTGGQQ HHHYDTHTNT YYLRTFGHNT IDAVPKIDFY RQTAAPLGEK L IRPTLSEL ...String:
MSASPPISAG DYLSAPEPDA LKPAGPTPSQ SRFQVDLVTE SAGDGETTVG FDSSPPEYVA EPPPDGLRDS VSGGEKAKGR FRVVNFAAS SPDAAPAETA QNGDTVMSEG SLHSSTGGQQ HHHYDTHTNT YYLRTFGHNT IDAVPKIDFY RQTAAPLGEK L IRPTLSEL HDELDKEPFE DGFANGEELT PAEESAAKDV SESKEPVRFG WVKGVMIRCM LNIWGVILYL RLPWITAQAG IV LTWIIIL LSVTVTSITG LSISAISTNG KVKSGGTYFL ISRSLGPELG GSIGLIFAFA NAVGVAMHTV GFAATVRDLL QEY GAPIVD PINDIRIIGV VSVTVLLAIS LAGMEWESKA QVLFFLVIMV SFANYLVGTL IPPSEDKASK GFFSYRADIF VQNL VPDWR GPDGTFFGMF SIFFPSATGI LAGANISGDL KDPAIAIPKG TLMAIFWTTI SYLAISATIG SCVVRDASGV LNDTV TPGW GACEGLACSY GWNFTECTQQ HSCHYGLINY YQTMSMVSGF APLITAGIFG ATLSSALACL VSAAKVFQCL CEDQLY PLI GFFGKGYGKN KEPVRGYLLA YAIAVAFIII AELNTIAPII SNFFLCSYAL INFSCFHASI TNSPGWRPSF QYYNKWA AL FGAIISVVIM FLLTWWAALI AIGVVLFLLL YVIYKKPEVN WGSSVQAGSY NLALSYSVGL NEVEDHIKNY RPQCLVLT G PPNFRPALVD FVGTFTRNLS LMICGHVLIG PHKQRMPELQ LIANGHTKWL NKRKIKAFYS DVIAEDLRRG VQILMQAAG LGRMKPNILV VGFKKNWQSA HPATVEDYIG ILHDAFDFNY GVCVMRMREG LNVSKMMQAH INPVFDPAED GKEASARVDP KALVKEEQA TTIFQSEQGK KTIDIYWLFD DGGLTLLIPY LLGRKRRWSK CKIRVFVGGQ INRMDQERKA IISLLSKFRL G FHEVHILP DINQNPRAEH TKRFEDMIAP FRLNDGFKDE ATVNEMRRDC PWKISDEEIT KNRVKSLRQV RLNEIVLDYS RD AALIVIT LPIGRKGKCP SSLYMAWLET LSQDLRPPVI LIRGNQENVL TFYCQ

UniProtKB: Solute carrier family 12 member 2, Solute carrier family 12 member 3

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: Polythiazide

MacromoleculeName: Polythiazide / type: ligand / ID: 3 / Number of copies: 2 / Formula: XZF
Molecular weightTheoretical: 439.882 Da
Chemical component information

ChemComp-XZF:
Polythiazide

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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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

Concentration12 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 196165
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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