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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 dataCryosparc sharpened map
Sample
  • Organelle or cellular component: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-gated ion channel 4
    • Protein or peptide: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
KeywordsION CHANNEL / PACEMAKER CURRENT / Structural Genomics / Structural Genomics Consortium / SGC / MEMBRANE PROTEIN
Function / homology
Function and homology information


voltage-gated potassium channel activity involved in SA node cell action potential depolarization / sinoatrial node development / HCN channels / regulation of cardiac muscle cell action potential involved in regulation of contraction / SA node cell action potential / membrane depolarization during SA node cell action potential / HCN channel complex / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / regulation of membrane depolarization ...voltage-gated potassium channel activity involved in SA node cell action potential depolarization / sinoatrial node development / HCN channels / regulation of cardiac muscle cell action potential involved in regulation of contraction / SA node cell action potential / membrane depolarization during SA node cell action potential / HCN channel complex / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / regulation of membrane depolarization / membrane depolarization during cardiac muscle cell action potential / sodium ion import across plasma membrane / blood circulation / voltage-gated sodium channel activity / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / monoatomic cation transport / voltage-gated potassium channel activity / regulation of cardiac muscle contraction / sodium ion transmembrane transport / cAMP binding / cellular response to cAMP / muscle contraction / potassium ion transmembrane transport / regulation of heart rate / regulation of membrane potential / axon / dendrite / perinuclear region of cytoplasm / identical protein binding / plasma membrane
Similarity search - Function
Ion transport N-terminal / Ion transport protein N-terminal / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / 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 ...Ion transport N-terminal / Ion transport protein N-terminal / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / 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
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsShintre CA / Pike ACW
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
History
DepositionJun 30, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseMay 8, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing 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
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  • 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

emd_0093.png

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)
AnnotationCryosparc sharpened map
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

Histogram

Histogram (log scale)
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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Mask #1

Fileemd_0093_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

Histogram

Histogram (log scale)

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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

Histogram

Histogram (log scale)

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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

Histogram

Histogram (log scale)

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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
Components
  • Organelle or cellular component: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-gated ion channel 4
    • Protein or peptide: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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Supramolecule #1: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-ga...

SupramoleculeName: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-gated ion channel 4
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Potassium/sodium hyperpolarization-activated cyclic nucleotide-ga...

MacromoleculeName: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.836754 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SMLPEAEVRL GQAGFMQRQF GAMLQPGVNK FSLRMFGSQK AVEREQERVK SAGFWIIHPY SDFRFYWDLT MLLLMVGNLI IIPVGITFF KDENTTPWIV FNVVSDTFFL IDLVLNFRTG IVVEDNTEII LDPQRIKMKY LKSWFMVDFI SSIPVDYIFL I VETRIDSE ...String:
SMLPEAEVRL GQAGFMQRQF GAMLQPGVNK FSLRMFGSQK AVEREQERVK SAGFWIIHPY SDFRFYWDLT MLLLMVGNLI IIPVGITFF KDENTTPWIV FNVVSDTFFL IDLVLNFRTG IVVEDNTEII LDPQRIKMKY LKSWFMVDFI SSIPVDYIFL I VETRIDSE VYKTARALRI VRFTKILSLL RLLRLSRLIR YIHQWEEIFH MTYDLASAVV RIVNLIGMML LLCHWDGCLQ FL VPMLQDF PDDCWVSINN MVNNSWGKQY SYALFKAMSH MLCIGYGRQA PVGMSDVWLT MLSMIVGATC YAMFIGHATA LIQ SLDSSR RQYQEKYKQV EQYMSFHKLP PDTRQRIHDY YEHRYQGKMF DEESILGELS EPLREEIINF NCRKLVASMP LFAN ADPNF VTSMLTKLRF EVFQPGDYII REGTIGKKMY FIQHGVVSVL TKGNKETKLA DGSYFGEICL LTRGRRTASV RADTY CRLY SLSVDNFNEV LEEYPMMRRA FETVALDRLD RIGKKNS

UniProtKB: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4

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Macromolecule #2: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 28 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #3: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 3 / Number of copies: 8 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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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

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMSodium chlorideNaCl
0.02 %DDM
0.002 %Cholesteryl hemisuccinate
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: blotted for 5.5s before plunge.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsEBIC TITAN KRIOS M02
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Number real images: 1294 / Average exposure time: 12.0 sec. / Average electron dose: 48.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 37313
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsImages were motioncorrected and dose-weighted with MOTIONCOR2
Particle selectionNumber selected: 157681
Details: Picking with templates derived from manually picked particles
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.6.5) / Number images used: 25764
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1-beta-0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1-beta-0)
Final 3D classificationNumber classes: 10 / Avg.num./class: 5324 / Software - Name: RELION (ver. 2.1-beta-0) / Details: Static classification with C4 symmetry imposed
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsModel refined against the cryosparc b-factor sharpened map using default restraints
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6gyn:
Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel

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