+Open data
-Basic information
Entry | Database: PDB / ID: 7tti | ||||||
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Title | Human KCC1 bound with VU0463271 In an outward-open state | ||||||
Components | Solute carrier family 12 member 4 | ||||||
Keywords | TRANSPORT PROTEIN/INHIBITOR / SLC12A4 / VU0463271 / Outward-open state / TRANSPORT PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information ammonium import across plasma membrane / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / ammonium channel activity / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / monoatomic ion transport / chloride transmembrane transport ...ammonium import across plasma membrane / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / ammonium channel activity / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / monoatomic ion transport / chloride transmembrane transport / potassium ion transmembrane transport / chemical synaptic transmission / lysosomal membrane / synapse / protein kinase binding / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Zhao, Y.X. / Cao, E.H. | ||||||
Funding support | 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: Structure of the human cation-chloride cotransport KCC1 in an outward-open state. Authors: Yongxiang Zhao / Jiemin Shen / Qinzhe Wang / Manuel Jose Ruiz Munevar / Pietro Vidossich / Marco De Vivo / Ming Zhou / Erhu Cao / Abstract: Cation-chloride cotransporters (CCCs) catalyze electroneutral symport of Cl with Na and/or K across membranes. CCCs are fundamental in cell volume homeostasis, transepithelia ion movement, ...Cation-chloride cotransporters (CCCs) catalyze electroneutral symport of Cl with Na and/or K across membranes. CCCs are fundamental in cell volume homeostasis, transepithelia ion movement, maintenance of intracellular Cl concentration, and neuronal excitability. Here, we present a cryoelectron microscopy structure of human K-Cl cotransporter (KCC)1 bound with the VU0463271 inhibitor in an outward-open state. In contrast to many other amino acid-polyamine-organocation transporter cousins, our first outward-open CCC structure reveals that opening the KCC1 extracellular ion permeation path does not involve hinge-bending motions of the transmembrane (TM) 1 and TM6 half-helices. Instead, rocking of TM3 and TM8, together with displacements of TM4, TM9, and a conserved intracellular loop 1 helix, underlie alternate opening and closing of extracellular and cytoplasmic vestibules. We show that KCC1 intriguingly exists in one of two distinct dimeric states via different intersubunit interfaces. Our studies provide a blueprint for understanding the mechanisms of CCCs and their inhibition by small molecule compounds. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tti.cif.gz | 221.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tti.ent.gz | 164.6 KB | Display | PDB format |
PDBx/mmJSON format | 7tti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tti_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7tti_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7tti_validation.xml.gz | 44.5 KB | Display | |
Data in CIF | 7tti_validation.cif.gz | 63.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/7tti ftp://data.pdbj.org/pub/pdb/validation_reports/tt/7tti | HTTPS FTP |
-Related structure data
Related structure data | 26116MC 7tthC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-11047 (Title: Cryo-EM structure of human KCC1 bound with inhibitor VU0463271 Data size: 3.9 TB Data #1: HumanKCC1-VU0463271 complex [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 120770.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC12A4, KCC1 / Production host: Homo sapiens (human) / References: UniProt: Q9UP95 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human potassium-chloride cotransporter 1 bound with VU0463271 Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20_4459: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Num. of particles: 81855 / Symmetry type: POINT | ||||||||||||||||||||||||
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