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- PDB-7yvc: Aplysia californica FaNaC in apo state -

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Basic information

Entry
Database: PDB / ID: 7yvc
TitleAplysia californica FaNaC in apo state
ComponentsFMRFamide-gated Na+ channel
KeywordsTRANSPORT PROTEIN / neuropeptide / ion channel / FMRFamide
Function / homologyEpithelial sodium channel / Amiloride-sensitive sodium channel / sodium channel activity / membrane / FMRFamide-gated Na+ channel
Function and homology information
Biological speciesAplysia californica (California sea hare)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,37522
Polymers229,9153
Non-polymers6,46019
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area23520 Å2
ΔGint20 kcal/mol
Surface area68090 Å2

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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: esidues 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): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q4TZI8
#2: 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: obtained synthetically
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
#3: 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 / N-Acetylglucosamine


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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
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 / 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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13FSC 0.143 CUT-OFF26900017YVCPOINT
23FSC 0.143 CUT-OFF26900017YVCPOINT
33FSC 0.143 CUT-OFF26900027YVCPOINT
43FSC 0.143 CUT-OFF26900027YVCPOINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 3 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00611904
ELECTRON MICROSCOPYf_angle_d0.79516104
ELECTRON MICROSCOPYf_dihedral_angle_d25.7061704
ELECTRON MICROSCOPYf_chiral_restr0.0641863
ELECTRON MICROSCOPYf_plane_restr0.0042037

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