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- EMDB-0093: Structure of human HCN4 hyperpolarization-activated cyclic nucleo... -

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Basic information

Entry
Database: EMDB / ID: EMD-0093
TitleStructure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel
Map data
SamplePotassium/Sodium hyperpolarization-activated cyclic nucleotide-gated ion channel 4
  • Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
  • (ligand) x 2
Function / homology
Function and homology information


voltage-gated potassium channel activity involved in SA node cell action potential depolarization / regulation of cardiac muscle cell action potential involved in regulation of contraction / HCN channel complex / membrane depolarization during SA node cell action potential / SA node cell action potential / intracellular cAMP-activated cation channel activity / membrane depolarization during cardiac muscle cell action potential / sodium ion import across plasma membrane / cellular response to cGMP / voltage-gated sodium channel activity ...voltage-gated potassium channel activity involved in SA node cell action potential depolarization / regulation of cardiac muscle cell action potential involved in regulation of contraction / HCN channel complex / membrane depolarization during SA node cell action potential / SA node cell action potential / intracellular cAMP-activated cation channel activity / membrane depolarization during cardiac muscle cell action potential / sodium ion import across plasma membrane / cellular response to cGMP / voltage-gated sodium channel activity / blood circulation / regulation of heart rate by cardiac conduction / potassium ion import across plasma membrane / sodium ion transmembrane transport / intrinsic component of plasma membrane / cation transport / potassium ion transmembrane transport / voltage-gated potassium channel activity / regulation of ion transmembrane transport / regulation of cardiac muscle contraction / cAMP binding / regulation of heart rate / regulation of membrane potential / cellular response to cAMP / muscle contraction / regulation of membrane depolarization / perinuclear region of cytoplasm / identical protein binding / plasma membrane
Cyclic nucleotide-binding domain / Cyclic nucleotide-binding-like / Ion transport domain / Ion transport N-terminal / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding, conserved site / RmlC-like jelly roll fold / Voltage-dependent channel domain superfamily / Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsShintre CA / Pike ACW / Tessitore A / Young M / Bushell SR / Strain-Damerell C / Mukhopadhyay S / Burgess-Brown NA / Huiskonen JT / Arrowsmith CH / Edwards AM / Bountra C / Carpenter EP / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/Z United Kingdom
European CommissionIMI 115766 United Kingdom
CitationJournal: To Be Published
Title: Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel
Authors: Shintre CA / Pike ACW / Tessitore A / Young M / Bushell SR / Strain-Damerell C / Mukhopadhyay S / Burgess-Brown NA / Huiskonen JT / Arrowsmith CH / Edwards AM / Bountra C / Carpenter EP
Validation ReportPDB-ID: 6gyn

SummaryFull reportAbout validation report
History
DepositionJun 30, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseMay 8, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6gyn
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0093.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 220 pix.
= 294.8 Å
1.34 Å/pix.
x 220 pix.
= 294.8 Å
1.34 Å/pix.
x 220 pix.
= 294.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.8
Minimum - Maximum-1.7871399 - 3.5708299
Average (Standard dev.)0.010690355 (±0.13185814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 294.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z294.800294.800294.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-1.7873.5710.011

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Supplemental data

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Segmentation: #1

Fileemd_0093_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Cryosparc unsharpened map

Fileemd_0093_additional.map
AnnotationCryosparc unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map1

Fileemd_0093_half_map_1.map
AnnotationHalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map2

Fileemd_0093_half_map_2.map
AnnotationHalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Potassium/Sodium hyperpolarization-activated cyclic nucleotide-ga...

EntireName: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-gated ion channel 4
Number of components: 4

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Component #1: cellular-component, Potassium/Sodium hyperpolarization-activated ...

Cellular-componentName: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-gated ion channel 4
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, Potassium/sodium hyperpolarization-activated cyclic nucl...

ProteinName: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 60.836754 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Number of Copies: 28 / Recombinant expression: No
MassTheoretical: 0.790145 kDa

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Component #4: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.748065 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 100 % / Details: blotted for 5.5s before plunge.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: EBIC TITAN KRIOS M02
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 48.7 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 37313.0 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1300.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1294

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 25764
Details: Images were motioncorrected and dose-weighted with MOTIONCOR2
3D reconstructionSoftware: cryoSPARC / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Details: Model refined against the cryosparc b-factor sharpened map using default restraints
Output model

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