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- EMDB-34122: Aplysia californica FaNaC in ligand bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-34122
TitleAplysia californica FaNaC in ligand bound state
Map dataligand bound full map
Sample
  • Complex: Trimeric FMRFamide activated sodium channel from Aplysia californica (AcFaNaC)
    • Protein or peptide: FMRFamide-gated Na+ channel
    • Protein or peptide: Phe-Met-Arg-Phe-amide
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsneuropeptide / ion channel / FMRFamide / TRANSPORT PROTEIN
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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsChen QF / Liu FL / Dang Y / Feng H / Zhang Z / Ye S
Funding support China, 2 items
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, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34122.png

Downloads & links

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Map

FileDownload / File: emd_34122.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationligand bound full map
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.07649527 - 0.16452333
Average (Standard dev.)0.00003229428 (±0.004055901)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: ligand bound half map 1

Fileemd_34122_half_map_1.map
Annotationligand bound half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ligand bound half map 2

Fileemd_34122_half_map_2.map
Annotationligand bound half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric FMRFamide activated sodium channel from Aplysia californ...

EntireName: Trimeric FMRFamide activated sodium channel from Aplysia californica (AcFaNaC)
Components
  • Complex: Trimeric FMRFamide activated sodium channel from Aplysia californica (AcFaNaC)
    • Protein or peptide: FMRFamide-gated Na+ channel
    • Protein or peptide: Phe-Met-Arg-Phe-amide
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Trimeric FMRFamide activated sodium channel from Aplysia californ...

SupramoleculeName: Trimeric FMRFamide activated sodium channel from Aplysia californica (AcFaNaC)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Aplysia californica (California sea hare)
Molecular weightTheoretical: 73 KDa

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Macromolecule #1: FMRFamide-gated Na+ channel

MacromoleculeName: FMRFamide-gated Na+ channel / type: protein_or_peptide / ID: 1
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.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Aplysia californica (California sea hare)
Molecular weightTheoretical: 76.638312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLGRGERIKP YHFRDSSADH MKYTSVSAKS GMVPEHRYTM VRSRHHGRHH HHHSYQEYNT QRSAISLIAE LGSESNAHGL AKIVTSRDT KRKVIWALMV IIGFTAATLQ LSLLVRKYLQ FQVVELSEIK DSMPVEYPSV TICNIEPISL RKIRKAYNKN E SQNLKDWL ...String:
MLGRGERIKP YHFRDSSADH MKYTSVSAKS GMVPEHRYTM VRSRHHGRHH HHHSYQEYNT QRSAISLIAE LGSESNAHGL AKIVTSRDT KRKVIWALMV IIGFTAATLQ LSLLVRKYLQ FQVVELSEIK DSMPVEYPSV TICNIEPISL RKIRKAYNKN E SQNLKDWL NFTQTFHFKD MSFMNSIRAF YENLGSDAKK ISHDLRDLLI HCRFNREECT TENFTSSFDG NYFNCFTFNG GQ LRDQLQM HATGPENGLS LIISIEKDEP LPGTYGVYNF ENNILHSAGV RVVVHAPGSM PSPVDHGFDI PPGYSSSVGL KAL LHTRLS EPYGNCTEDS LEGIQTYRNT FFACLQLCKQ RRLIRECKCK SSALPDLSVE NITFCGVIPD WKDIRRNVTG EYKM NQTIP TISLACEARV QKQLNNDRSY ETECGCYQPC SETSYLKSVS LSYWPLEFYQ LSALERFFSQ KNPTDQQHFM KIAQD FLSR LAHPQQQALA RNNSHDKDIL TTSYSLSEKE MAKEASDLIR QNLLRLNIYL EDLSVVEYRQ LPAYGLADLF ADIGGT LGL WMGISVLTIM ELMELIIRLF ALIFNAEREV PKAPVHSSNN GGGGGGDGQH NFANGDVEHE RDTHFPDLGS SDFDFRR GG GIGAESPVNV EGGSSGGLVP RGSGGSSGGH HHHHHHH

UniProtKB: FMRFamide-gated Na+ channel

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Macromolecule #2: Phe-Met-Arg-Phe-amide

MacromoleculeName: Phe-Met-Arg-Phe-amide / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 599.767 Da
SequenceString:
FMR(NFA)

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration4.00 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Average electron dose: 60.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Average electron dose: 60.0 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: GATAN K3 (6k x 4k) / #2 - Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 267000
Image processing ID1
Image recording ID1

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Image processing #2

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 267000
Image processing ID2
Image recording ID2

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Image processing #3

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 267000
Image processing ID3
Image recording ID3

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Image processing #4

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 267000
Image processing ID4
Image recording ID1

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

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

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