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- PDB-6gyo: Structure of human HCN4 hyperpolarization-activated cyclic nucleo... -

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Entry
Database: PDB / ID: 6gyo
TitleStructure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel in complex with cAMP
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
KeywordsMEMBRANE PROTEIN / ION CHANNEL / PACEMAKER CURRENT
Function / homology
Function and homology information


HCN channels / 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 / membrane depolarization during SA node cell action potential / SA node cell action potential / HCN channel complex / intracellular cAMP-activated cation channel activity / membrane depolarization during cardiac muscle cell action potential / sodium ion import across plasma membrane / cellular response to cGMP ...HCN channels / 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 / membrane depolarization during SA node cell action potential / SA node cell action potential / HCN channel complex / 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 / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / sodium ion transmembrane transport / blood circulation / cation transport / intrinsic component of plasma membrane / potassium ion transmembrane transport / regulation of ion transmembrane transport / voltage-gated potassium channel activity / regulation of cardiac muscle contraction / cAMP binding / regulation of membrane potential / muscle contraction / regulation of heart rate / cellular response to cAMP / regulation of membrane depolarization / perinuclear region of cytoplasm / identical protein binding / plasma membrane
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 / Cyclic nucleotide-binding domain signature 1. / Voltage-dependent channel domain superfamily / Cyclic nucleotide-binding-like / Cyclic nucleotide-binding, conserved site / RmlC-like jelly roll fold / Ion transport N-terminal / Ion transport domain / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding domain ...Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 / Cyclic nucleotide-binding domain signature 1. / Voltage-dependent channel domain superfamily / Cyclic nucleotide-binding-like / Cyclic nucleotide-binding, conserved site / RmlC-like jelly roll fold / Ion transport N-terminal / Ion transport domain / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding domain / Ion transport protein / Cyclic nucleotide-binding domain / Ion transport protein N-terminal / cAMP/cGMP binding motif profile.
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsShintre, C.A. / Pike, A.C.W. / Tessitore, A. / Young, M. / Bushell, S.R. / Strain-Damerell, C. / Mukhopadhyay, S. / Burgess-Brown, N.A. / Huiskonen, J.T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding supportUnited Kingdom , 2件
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/ZUnited Kingdom
European CommissionIMI 115766United Kingdom
CitationJournal: To Be Published
Title: Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel
Authors: Shintre, C.A. / Pike, A.C.W. / Tessitore, A. / Young, M. / Bushell, S.R. / Strain-Damerell, C. / Mukhopadhyay, S. / Burgess-Brown, N.A. / Huiskonen, J.T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 30, 2018 / Release: May 1, 2019Array

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Assembly

Deposited unit
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
C: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
D: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,37852
Polymers243,3474
Non-polymers33,03148
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area64080 Å2
ΔGint-626 kcal/mol
Surface area85640 Å2
MethodPISA

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Components

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Protein/peptide , 1 types, 4 molecules ABCD

#1: Protein/peptide
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4


Mass: 60836.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCN4 / Plasmid: pFB-LIC-Bse / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y3Q4

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Non-polymers , 5 types, 48 molecules

#2: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N5O6P / Cyclic adenosine monophosphate
#3: Chemical...
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid *YM
#4: Chemical
ChemComp-PIE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL


Mass: 836.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C43H80O13P
#5: Chemical
ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid *YM
#6: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-gated ion channel 4
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer component

Buffer-ID: 1

IDConc.NameFormula
120 mMHEPES
2150 mMSodium chlorideNaCl
30.02 %DDM
40.002 %Cholesteryl hemisuccinate
55 mMcyclic AMPCyclic adenosine monophosphate
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K / Details: blotted for 5.5s before plunge

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: EBIC TITAN KRIOS M07
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 37313 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1300 nm
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 16 sec. / Electron dose: 48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2338
Image scansMovie frames/image: 48 / Used frames/image: 1-48

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1Gautomatch0.53particle selection
2EPUimage acquisition
4CTFFIND4.1.5CTF correction
7Coot0.8.9.1model fitting
9RELION2.1-beta-0initial Euler assignment
10RELION2.1-beta-0final Euler assignment
11RELION2.1-beta-0classification
12cryoSPARC0.6.53D reconstruction
13PHENIX1.13model refinement
Image processingDetails: Images were motioncorrected and dose-weighted with MOTIONCOR2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 234908
Details: Autopicking with templates derived from manually picked particles
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55829 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Details: Initial model was from ligand-free HCN4. Model refined against the cryosparc b-factor sharpened map using default restraints

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