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- EMDB-8632: CryoEM Structure of a Prokaryotic Cyclic Nucleotide-Gated Ion Channel -

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Basic information

Entry
Database: EMDB / ID: 8632
TitleCryoEM Structure of a Prokaryotic Cyclic Nucleotide-Gated Ion Channel
Map dataProkaryotic Cyclic Nucleotide-Gated Ion Channel
SampleLliK
  • Transporter, cation channel family / cyclic nucleotide-binding domain multi-domain protein
Function/homologyPotassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / voltage-gated potassium channel activity / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding-like / Ion transport domain / Cyclic nucleotide-binding domain / Ion transport protein ...Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / voltage-gated potassium channel activity / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding-like / Ion transport domain / Cyclic nucleotide-binding domain / Ion transport protein / RmlC-like jelly roll fold / integral component of membrane / Transporter, cation channel family / cyclic nucleotide-binding domain multi-domain protein
Function and homology information
SourceLeptospira licerasiae serovar varillal str. var 010 / / bacteria
MethodCryo EM / single particle reconstruction / 4.2 Å resolution
AuthorsJames ZM / Borst AJ
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel.
Authors: Zachary M James / Andrew J Borst / Yoni Haitin / Brandon Frenz / Frank DiMaio / William N Zagotta / David Veesler
Abstract: Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) ion channels play crucial physiological roles in phototransduction, olfaction, and cardiac pace making. ...Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) ion channels play crucial physiological roles in phototransduction, olfaction, and cardiac pace making. These channels are characterized by the presence of a carboxyl-terminal cyclic nucleotide-binding domain (CNBD) that connects to the channel pore via a C-linker domain. Although cyclic nucleotide binding has been shown to promote CNG and HCN channel opening, the precise mechanism underlying gating remains poorly understood. Here we used cryoEM to determine the structure of the intact LliK CNG channel isolated from -which shares sequence similarity to eukaryotic CNG and HCN channels-in the presence of a saturating concentration of cAMP. A short S4-S5 linker connects nearby voltage-sensing and pore domains to produce a non-domain-swapped transmembrane architecture, which appears to be a hallmark of this channel family. We also observe major conformational changes of the LliK C-linkers and CNBDs relative to the crystal structures of isolated C-linker/CNBD fragments and the cryoEM structures of related CNG, HCN, and KCNH channels. The conformation of our LliK structure may represent a functional state of this channel family not captured in previous studies.
Validation ReportPDB-ID: 5v4s

SummaryFull reportAbout validation report
DateDeposition: Mar 10, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: Apr 12, 2017 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.088
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.088
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5v4s
  • Surface level: 0.088
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

emd_8632.png

Downloads & links

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Map

Fileemd_8632.map.gz (map file in CCP4 format, 49949 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
232 pix
1.37 Å/pix.
= 316.796 Å		232 pix
1.37 Å/pix.
= 316.796 Å		232 pix
1.37 Å/pix.
= 316.796 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.3655 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.088 (by author), 0.088 (movie #1):
Minimum - Maximum-0.25903082 - 0.44441
Average (Standard dev.)0.0007262135 (0.009121994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions232232232
Origin000
Limit231231231
Spacing232232232
CellA=B=C: 316.796 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.36551.36551.3655
M x/y/z232232232
origin x/y/z0.0000.0000.000
length x/y/z316.796316.796316.796
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS232232232
D min/max/mean-0.2590.4440.001

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Supplemental data

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Sample components

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Entire LliK

EntireName: LliK / Number of components: 2
MassTheoretical: 200 kDa

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Component #1: protein, LliK

ProteinName: LliK / Recombinant expression: No
MassTheoretical: 200 kDa
SourceSpecies: Leptospira licerasiae serovar varillal str. var 010 / / bacteria
Source (engineered)Expression System: Escherichia coli / / bacteria /

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Component #2: protein, Transporter, cation channel family / cyclic nucleotide-b...

ProteinName: Transporter, cation channel family / cyclic nucleotide-binding domain multi-domain protein
Recombinant expression: No
MassTheoretical: 53.464785 kDa
Source (engineered)Expression System: Leptospira licerasiae serovar varillal str. var 010 / / bacteria

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: Cryo EM
Sample solutionSpecimen conc.: 0.9 mg/ml / pH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 18737
3D reconstructionSoftware: RELION / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

5v4s

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