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- EMDB-34123: Aplysia californica FaNaC in apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-34123
TitleAplysia californica FaNaC in apo state
Map dataApo state full map
Sample
  • Complex: Trimeric FMRFamide activated sodium channel from Aplysia californica (AcFaNaC)
    • Protein or peptide: FMRFamide-gated Na+ channel
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
Keywordsneuropeptide / ion channel / FMRFamide / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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_34123.png

Downloads & links

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Map

FileDownload / File: emd_34123.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApo state full map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 256 pix.
= 296.96 Å		1.16 Å/pix.
x 256 pix.
= 296.96 Å		1.16 Å/pix.
x 256 pix.
= 296.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.06131265 - 0.1415866
Average (Standard dev.)0.0000036444387 (±0.0030717233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 296.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Apo state half map 1

Fileemd_34123_half_map_1.map
AnnotationApo state half map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Apo state half map 2

Fileemd_34123_half_map_2.map
AnnotationApo state half map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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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
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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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
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: 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.
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 #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 269000
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING

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Image processing #2

Image processing ID2
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 269000
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7yvc:
Aplysia californica FaNaC in apo state

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