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- EMDB-6657: Structure of a eukaryotic cyclic nucleotide-gated channel -

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Basic information

Entry
Database: EMDB / ID: EMD-6657
TitleStructure of a eukaryotic cyclic nucleotide-gated channel
Map dataTAX-4 density map without symmetry imposed after post-processing in RELION1.4. The reported resolution is 4.5A.
Sample
  • Complex: Cyclic nucleotide-gated (CNG) channels
    • Protein or peptide: Cyclic nucleotide-gated (CNG) channels
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsLi X
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-
UpdateAug 29, 2018-
Current statusAug 29, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0376
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0376
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6657.png

Downloads & links

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Map

FileDownload / File: emd_6657.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTAX-4 density map without symmetry imposed after post-processing in RELION1.4. The reported resolution is 4.5A.
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.0376 / Movie #1: 0.0376
Minimum - Maximum-0.10155387 - 0.15939233
Average (Standard dev.)0.0009718568 (±0.0074000903)
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-0.1020.1590.001

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Supplemental data

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Additional map: TAX-4 density map without symmetry imposed before post-processing...

Fileemd_6657_additional.map
AnnotationTAX-4 density map without symmetry imposed before post-processing in RELION1.4. The reported resolution is 5.1A.
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 (CNG) channels

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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: all
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant plasmid: pFastBac1

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

MacromoleculeName: Cyclic nucleotide-gated (CNG) channels / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GGGGSMSTAE PAPDPTNPST SGLAPTTNGI GSPPPTASAA TKFSILTKFL RRKNQVHTTT AQQNEFMQKY MPNGNSNAVQ PAATGGQPAS SDGGSAIEVP PPKESYAVRI RKYLANYTQD PSTDNFYYWT CVVTVAYIYN LLFVIARQVF NDLIGPSSQS LCRFYNGTLN ...String:
GGGGSMSTAE PAPDPTNPST SGLAPTTNGI GSPPPTASAA TKFSILTKFL RRKNQVHTTT AQQNEFMQKY MPNGNSNAVQ PAATGGQPAS SDGGSAIEVP PPKESYAVRI RKYLANYTQD PSTDNFYYWT CVVTVAYIYN LLFVIARQVF NDLIGPSSQS LCRFYNGTLN STTQVECTYN MLTNMKEMPT YSQYPDLGWS KYWHFRMLWV FFDLLMDCVY LIDTFLNYRM GYMDQGLVVR EAEKVTKAYW QSKQYRIDGI SLIPLDYILG WPIPYINWRG LPILRLNRLI RYKRVRNCLE RTETRSSMPN AFRVVVVVWY IVIIIHWNAC LYFWISEWIG LGTDAWVYGH LNKQSLPDDI TDTLLRRYVY SFYWSTLILT TIGEVPSPVR NIEYAFVTLD LMCGVLIFAT IVGNVGSMIS NMSAARTEFQ NKMDGIKQYM ELRKVSKQLE IRVIKWFDYL WTNKQSLSDQ QVLKVLPDKL QAEIAMQVHF ETLRKVRIFQ DCEAGLLAEL VLKLQLQVFS PGDFICKKGD IGREMYIVKR GRLQVVDDDG KKVFVTLQEG SVFGELSILN IAGSKNGNRR TANVRSVGYT DLFVLSKTDL WNALREYPDA RKLLLAKGRE ILKKDNLLDE NAPEEQKTVE EIAEHLNNAV KVLQTRMARL IVEHSSTEGK LMKRIEMLEK HLSRYKALAR RQKTMHGVSI DGGDISTDGV DERVRPPRLR QTKTIDLPTG TESESLLK

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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 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 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 99934

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