+Open data
-Basic information
Entry | Database: PDB / ID: 7yvb | |||||||||
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Title | Aplysia californica FaNaC in ligand bound state | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / neuropeptide / ion channel / FMRFamide | |||||||||
Function / homology | Epithelial sodium channel / Amiloride-sensitive sodium channel / ligand-gated sodium channel activity / membrane / FMRFamide-gated Na+ channel Function and homology information | |||||||||
Biological species | Aplysia californica (California sea hare) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Chen, Q.F. / Liu, F.L. / Dang, Y. / Feng, H. / Zhang, Z. / Ye, S. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Chem Biol / Year: 2023 Title: Structure and mechanism of a neuropeptide-activated channel in the ENaC/DEG superfamily. Authors: Fenglian Liu / Yu Dang / Lu Li / Hao Feng / Jianlin Li / Haowei Wang / Xu Zhang / Zhe Zhang / Sheng Ye / Yutao Tian / Qingfeng Chen / Abstract: Phe-Met-Arg-Phe-amide (FMRFamide)-activated sodium channels (FaNaCs) are a family of channels activated by the neuropeptide FMRFamide, and, to date, the underlying ligand gating mechanism remains ...Phe-Met-Arg-Phe-amide (FMRFamide)-activated sodium channels (FaNaCs) are a family of channels activated by the neuropeptide FMRFamide, and, to date, the underlying ligand gating mechanism remains unknown. Here we present the high-resolution cryo-electron microscopy structures of Aplysia californica FaNaC in both apo and FMRFamide-bound states. AcFaNaC forms a chalice-shaped trimer and possesses several notable features, including two FaNaC-specific insertion regions, a distinct finger domain and non-domain-swapped transmembrane helix 2 in the transmembrane domain (TMD). One FMRFamide binds to each subunit in a cleft located in the top-most region of the extracellular domain, with participation of residues from the neighboring subunit. Bound FMRFamide adopts an extended conformation. FMRFamide binds tightly to A. californica FaNaC in an N terminus-in manner, which causes collapse of the binding cleft and induces large local conformational rearrangements. Such conformational changes are propagated downward toward the TMD via the palm domain, possibly resulting in outward movement of the TMD and dilation of the ion conduction pore. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yvb.cif.gz | 274.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yvb.ent.gz | 221.4 KB | Display | PDB format |
PDBx/mmJSON format | 7yvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yvb_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7yvb_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7yvb_validation.xml.gz | 52.3 KB | Display | |
Data in CIF | 7yvb_validation.cif.gz | 76.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/7yvb ftp://data.pdbj.org/pub/pdb/validation_reports/yv/7yvb | HTTPS FTP |
-Related structure data
Related structure data | 34122MC 7yvcC 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 |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 76638.312 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Residues 672-679 correspond to the EXPRESSION TAG, whereas resides 660-665 correspond to the thrombin cleavage site, and resides 654-659 and 666-671 correspond to flexible linkers. Source: (gene. exp.) Aplysia californica (California sea hare) Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q4TZI8 #2: Protein/peptide | Mass: 599.767 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: 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 #4: Sugar | ChemComp-NAG / 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: Trimeric FMRFamide activated sodium channel from Aplysia californica (AcFaNaC) Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.073 MDa / Experimental value: NO |
Source (natural) | Organism: Aplysia californica (California sea hare) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293F / Plasmid: pEZT-BM |
Buffer solution | pH: 8 |
Specimen | Conc.: 4 mg/ml / 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: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm | ||||||||||||||||
Image recording |
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-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Image processing |
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CTF correction |
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3D reconstruction |
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Atomic model building | Protocol: AB INITIO MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 2.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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