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- PDB-2mng: Apo Structure of human HCN4 CNBD solved by NMR -

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Basic information

Entry
Database: PDB / ID: 2mng
TitleApo Structure of human HCN4 CNBD solved by NMR
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
KeywordsTRANSPORT PROTEIN / Cyclic AMP binding domain / CS-ROSETTA
Function / homology
Function and homology information


voltage-gated potassium channel activity involved in SA node cell action potential depolarization / sinoatrial node development / HCN channels / HCN channel complex / 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 / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / membrane depolarization during cardiac muscle cell action potential ...voltage-gated potassium channel activity involved in SA node cell action potential depolarization / sinoatrial node development / HCN channels / HCN channel complex / 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 / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / membrane depolarization during cardiac muscle cell action potential / sodium ion import across plasma membrane / blood circulation / voltage-gated sodium channel activity / regulation of membrane depolarization / potassium ion import across plasma membrane / voltage-gated potassium channel activity / regulation of heart rate by cardiac conduction / monoatomic cation transport / sodium ion transmembrane transport / regulation of cardiac muscle contraction / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / regulation of heart rate / regulation of membrane potential / muscle contraction / 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 / Cyclic nucleotide-binding domain superfamily ...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 / Jelly Rolls / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model detailsclosest to the average, model10
AuthorsAkimoto, M. / Zhang, Z. / Boulton, S. / Selvaratnam, R. / VanSchouwen, B. / Gloyd, M. / Accili, E.A. / Lange, O.F. / Melacini, G.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A mechanism for the auto-inhibition of hyperpolarization-activated cyclic nucleotide-gated (HCN) channel opening and its relief by cAMP.
Authors: Akimoto, M. / Zhang, Z. / Boulton, S. / Selvaratnam, R. / VanSchouwen, B. / Gloyd, M. / Accili, E.A. / Lange, O.F. / Melacini, G.
History
DepositionApr 3, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4


Theoretical massNumber of molelcules
Total (without water)14,9851
Polymers14,9851
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 14985.237 Da / Num. of mol.: 1 / Fragment: Cyclic AMP binding domain (UNP residues 579-707)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCN4 / Plasmid: pET302NT-His / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3Q4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D H(CCO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D (H)CCH-TOCSY
1813D C(CO)NH
1922D 1H-15N HSQC
11032D 1H-15N HSQC
NMR detailsText: The structure was determined using chemical shift and residual dipolar coupling data.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM DTT, 20 mM MES, 100 mM potassium chloride, 2 mM EDTA, 2 mM EGTA, 0.02% sodium azide, 0.5 mM [U-13C; U-15N] Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4, 95% H2O/5% D2O95% H2O/5% D2O
21 mM DTT, 20 mM MES, 100 mM potassium chloride, 1 mM EDTA, 0.02% sodium azide, 0.2 mM [U-15N] Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4, 6 mg/mL Pf1 phage, 95% H2O/5% D2O95% H2O/5% D2O
31 mM DTT, 20 mM MES, 100 mM potassium chloride, 1 mM EDTA, 0.02% sodium azide, 0.2 mM [U-15N] Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDTT-11
20 mMMES-21
100 mMpotassium chloride-31
2 mMEDTA-41
2 mMEGTA-51
0.02 %sodium azide-61
0.5 mMPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4-7[U-13C; U-15N]1
1 mMDTT-82
20 mMMES-92
100 mMpotassium chloride-102
1 mMEDTA-112
0.02 %sodium azide-122
0.2 mMPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4-13[U-15N]2
6 mg/mLPf1 phage-142
1 mMDTT-153
20 mMMES-163
100 mMpotassium chloride-173
1 mMEDTA-183
0.02 %sodium azide-193
0.2 mMPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4-20[U-15N]3
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8502

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
RosettaLange and Bakerrefinement
RefinementSoftware ordinal: 1 / Details: RASREC-Rosetta, Lange & Baker, 2012, Proteins
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50000 / Conformers submitted total number: 10

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