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- EMDB-6656: Structure of a eukaryotic cyclic nucleotide-gated channel -

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Basic information

Entry
Database: EMDB / ID: EMD-6656
TitleStructure of a eukaryotic cyclic nucleotide-gated channel
Map dataTAX-4 density map with C4 symmetry imposed after post-processing in RELION1.4.The reported resolution is 3.5 angstroms.
Sample
  • Complex: Cyclic nucleotide-gated (CNG) channels
    • Protein or peptide: Cyclic nucleotide-gated cation channel
  • Ligand: CYCLIC GUANOSINE MONOPHOSPHATE
  • Ligand: SODIUM IONSodium
Function / homology
Function and homology information


detection of carbon dioxide / detection of chemical stimulus involved in sensory perception / ciliary inversin compartment / Activation of the phototransduction cascade / Inactivation, recovery and regulation of the phototransduction cascade / VxPx cargo-targeting to cilium / thermosensory behavior / positive regulation of growth rate / olfactory behavior / intracellular cyclic nucleotide activated cation channel complex ...detection of carbon dioxide / detection of chemical stimulus involved in sensory perception / ciliary inversin compartment / Activation of the phototransduction cascade / Inactivation, recovery and regulation of the phototransduction cascade / VxPx cargo-targeting to cilium / thermosensory behavior / positive regulation of growth rate / olfactory behavior / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / chemosensory behavior / aerotaxis / intracellularly cAMP-activated cation channel activity / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / response to oxygen levels / cation channel complex / thermotaxis / multicellular organismal reproductive process / non-motile cilium / regulation of axon extension / regulation of neuron differentiation / negative regulation of cGMP-mediated signaling / monoatomic cation transmembrane transport / voltage-gated potassium channel activity / phototransduction / cGMP binding / response to hyperoxia / neuron projection morphogenesis / calcium-mediated signaling / chemotaxis / dendrite / protein-containing complex binding / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / membrane / identical protein binding / plasma membrane
Similarity search - Function
Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Cyclic nucleotide-gated cation channel
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLi M / Zhou X / Wang S / Michailidis I / Gong Y / Su D / Li H / Li X / Yang J
Funding support United States, China, 15 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM085234 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)RO1NS053494 United States
National Basic Research Program of China2014CB910301 China
National Natural Science Foundation of China31370821 China
Top Talents of Program of Yunnan Province2011HA012 China
High-level Overseas Talents of Yunnan Province China
China Youth 1000-talent Program of the State Council of China China
Beijing Advanced Innovation Center for Structural Biology China
Tsinghua-Peking Joint Center for Life Sciences China
National Natural Science Foundation of China31570730 China
Key Research Program of the Chinese Academy of SciencesKJZD-EW-L03 China
National Natural Science Foundation of China81302865 China
West Light Foundation of the Chinese Academy of Sciences China
Yunnan Applied Basic Research Projects2013FB074 China
Youth Innovation Promotion Association of the Chinese Academy of Sciences China
CitationJournal: Nature / Year: 2017
Title: Structure of a eukaryotic cyclic-nucleotide-gated channel.
Authors: Minghui Li / Xiaoyuan Zhou / Shu Wang / Ioannis Michailidis / Ye Gong / Deyuan Su / Huan Li / Xueming Li / Jian Yang /
Abstract: Cyclic-nucleotide-gated channels are essential for vision and olfaction. They belong to the voltage-gated ion channel superfamily but their activities are controlled by intracellular cyclic ...Cyclic-nucleotide-gated channels are essential for vision and olfaction. They belong to the voltage-gated ion channel superfamily but their activities are controlled by intracellular cyclic nucleotides instead of transmembrane voltage. Here we report a 3.5-Å-resolution single-particle electron cryo-microscopy structure of a cyclic-nucleotide-gated channel from Caenorhabditis elegans in the cyclic guanosine monophosphate (cGMP)-bound open state. The channel has an unusual voltage-sensor-like domain, accounting for its deficient voltage dependence. A carboxy-terminal linker connecting S6 and the cyclic-nucleotide-binding domain interacts directly with both the voltage-sensor-like domain and the pore domain, forming a gating ring that couples conformational changes triggered by cyclic nucleotide binding to the gate. The selectivity filter is lined by the carboxylate side chains of a functionally important glutamate and three rings of backbone carbonyls. This structure provides a new framework for understanding mechanisms of ion permeation, gating and channelopathy of cyclic-nucleotide-gated channels and cyclic nucleotide modulation of related channels.
History
DepositionOct 26, 2016-
Header (metadata) releaseJan 25, 2017-
Map releaseJan 25, 2017-
UpdateMar 23, 2022-
Current statusMar 23, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0426
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0426
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5h3o
  • Surface level: 0.0426
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6656.png

Downloads & links

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Map

FileDownload / File: emd_6656.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTAX-4 density map with C4 symmetry imposed after post-processing in RELION1.4.The reported resolution is 3.5 angstroms.
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.0426 / Movie #1: 0.0426
Minimum - Maximum-0.1948873 - 0.34038877
Average (Standard dev.)0.0007895406 (±0.010400022)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 211.20001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z211.200211.200211.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1950.3400.001

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Supplemental data

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Additional map: TAX-4 density map with C4 symmetry imposed before...

Fileemd_6656_additional.map
AnnotationTAX-4 density map with C4 symmetry imposed before post-processing in RELION1.4.The reported resolution is 3.9 angstroms.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cyclic nucleotide-gated (CNG) channels

EntireName: Cyclic nucleotide-gated (CNG) channels
Components
  • Complex: Cyclic nucleotide-gated (CNG) channels
    • Protein or peptide: Cyclic nucleotide-gated cation channel
  • Ligand: CYCLIC GUANOSINE MONOPHOSPHATE
  • Ligand: SODIUM IONSodium

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Supramolecule #1: Cyclic nucleotide-gated (CNG) channels

SupramoleculeName: Cyclic nucleotide-gated (CNG) channels / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant plasmid: pFastBac1

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Macromolecule #1: Cyclic nucleotide-gated cation channel

MacromoleculeName: Cyclic nucleotide-gated cation channel / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 84.305898 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GGGGSMSTAE PAPDPTNPST SGLAPTTNGI GSPPPTASAA TKFSILTKFL RRKNQVHTTT AQQNEFMQKY MPNGNSNAVQ PAATGGQPA SSDGGSAIEV PPPKESYAVR IRKYLANYTQ DPSTDNFYYW TCVVTVAYIY NLLFVIARQV FNDLIGPSSQ S LCRFYNGT ...String:
GGGGSMSTAE PAPDPTNPST SGLAPTTNGI GSPPPTASAA TKFSILTKFL RRKNQVHTTT AQQNEFMQKY MPNGNSNAVQ PAATGGQPA SSDGGSAIEV PPPKESYAVR IRKYLANYTQ DPSTDNFYYW TCVVTVAYIY NLLFVIARQV FNDLIGPSSQ S LCRFYNGT LNSTTQVECT YNMLTNMKEM PTYSQYPDLG WSKYWHFRML WVFFDLLMDC VYLIDTFLNY RMGYMDQGLV VR EAEKVTK AYWQSKQYRI DGISLIPLDY ILGWPIPYIN WRGLPILRLN RLIRYKRVRN CLERTETRSS MPNAFRVVVV VWY IVIIIH WNACLYFWIS EWIGLGTDAW VYGHLNKQSL PDDITDTLLR RYVYSFYWST LILTTIGEVP SPVRNIEYAF VTLD LMCGV LIFATIVGNV GSMISNMSAA RTEFQNKMDG IKQYMELRKV SKQLEIRVIK WFDYLWTNKQ SLSDQQVLKV LPDKL QAEI AMQVHFETLR KVRIFQDCEA GLLAELVLKL QLQVFSPGDF ICKKGDIGRE MYIVKRGRLQ VVDDDGKKVF VTLQEG SVF GELSILNIAG SKNGNRRTAN VRSVGYTDLF VLSKTDLWNA LREYPDARKL LLAKGREILK KDNLLDENAP EEQKTVE EI AEHLNNAVKV LQTRMARLIV EHSSTEGKLM KRIEMLEKHL SRYKALARRQ KTMHGVSIDG GDISTDGVDE RVRPPRLR Q TKTIDLPTGT ESESLLK

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Macromolecule #2: CYCLIC GUANOSINE MONOPHOSPHATE

MacromoleculeName: CYCLIC GUANOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: PCG
Molecular weightTheoretical: 345.205 Da
Chemical component information

ChemComp-PCG:
CYCLIC GUANOSINE MONOPHOSPHATE / Cyclic guanosine monophosphate

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 3
Molecular weightTheoretical: 22.99 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

Concentration0.6 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMC8H18N2O4S4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
2.0 mMC10H12N5O7PcGMP
2.0 mMHSCH2CH2OH2-Mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blotted for 4.0 seconds (double-sided, blot force 1), after waiting for 3.0 seconds the grid was immediately plunged into liquid ethane cooled by liquid-nitrogen..
DetailsThis sample was homogeneous

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-32 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: OTHER
Details: A TRP channel (unpublished) which was low-pass filtered to 60 angstroms was used as the initial model.
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationSoftware - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 99934

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