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- PDB-7yvb: Aplysia californica FaNaC in ligand bound state -

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Basic information

Entry
Database: PDB / ID: 7yvb
TitleAplysia californica FaNaC in ligand bound state
Components
  • FMRFamide-gated Na+ channel
  • Phe-Met-Arg-Phe-amide
KeywordsTRANSPORT PROTEIN / neuropeptide / ion channel / FMRFamide
Function / homologyEpithelial sodium channel / Amiloride-sensitive sodium channel / ligand-gated sodium channel activity / membrane / FMRFamide-gated Na+ channel
Function and homology information
Biological speciesAplysia californica (California sea hare)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsChen, Q.F. / Liu, F.L. / Dang, Y. / Feng, H. / Zhang, Z. / Ye, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071202 China
National Natural Science Foundation of China (NSFC)32171201 China
CitationJournal: 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
DepositionAug 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMRFamide-gated Na+ channel
B: FMRFamide-gated Na+ channel
C: FMRFamide-gated Na+ channel
P: Phe-Met-Arg-Phe-amide
Q: Phe-Met-Arg-Phe-amide
R: Phe-Met-Arg-Phe-amide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,13424
Polymers231,7146
Non-polymers6,42018
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein FMRFamide-gated Na+ channel


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 Phe-Met-Arg-Phe-amide


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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Trimeric FMRFamide activated sodium channel from Aplysia californica (AcFaNaC)
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 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 solutionpH: 8
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1160GATAN K3 (6k x 4k)
2160GATAN K3 (6k x 4k)
3160GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
Image processing
IDImage recording-ID
11
22
33
41
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
33PHASE FLIPPING AND AMPLITUDE CORRECTION
44PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
12.9FSC 0.143 CUT-OFF26700017YVBPOINT
22.9FSC 0.143 CUT-OFF26700017YVBPOINT
32.9FSC 0.143 CUT-OFF26700017YVBPOINT
42.9FSC 0.143 CUT-OFF26700017YVBPOINT
52.9FSC 0.143 CUT-OFF26700027YVBPOINT
62.9FSC 0.143 CUT-OFF26700027YVBPOINT
72.9FSC 0.143 CUT-OFF26700027YVBPOINT
82.9FSC 0.143 CUT-OFF26700027YVBPOINT
92.9FSC 0.143 CUT-OFF26700037YVBPOINT
102.9FSC 0.143 CUT-OFF26700037YVBPOINT
112.9FSC 0.143 CUT-OFF26700037YVBPOINT
122.9FSC 0.143 CUT-OFF26700037YVBPOINT
133FSC 0.143 CUT-OFF26700047YVBPOINT
142.9FSC 0.143 CUT-OFF26700047YVBPOINT
152.9FSC 0.143 CUT-OFF26700047YVBPOINT
162.9FSC 0.143 CUT-OFF26700047YVBPOINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 2.9 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00512138
ELECTRON MICROSCOPYf_angle_d0.75516413
ELECTRON MICROSCOPYf_dihedral_angle_d24.1631770
ELECTRON MICROSCOPYf_chiral_restr0.0471890
ELECTRON MICROSCOPYf_plane_restr0.0042076

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