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- PDB-2mpf: Solution structure human HCN2 CNBD in the cAMP-unbound state -

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Basic information

Entry
Database: PDB / ID: 2mpf
TitleSolution structure human HCN2 CNBD in the cAMP-unbound state
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
KeywordsTRANSPORT PROTEIN / HCN channels
Function / homology
Function and homology information


HCN channels / HCN channel complex / ammonium transmembrane transport / 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 / voltage-gated sodium channel activity / potassium ion import across plasma membrane ...HCN channels / HCN channel complex / ammonium transmembrane transport / 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 / voltage-gated sodium channel activity / potassium ion import across plasma membrane / voltage-gated potassium channel activity / sodium ion transmembrane transport / voltage-gated potassium channel complex / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / regulation of membrane potential / cell-cell signaling / axon / dendrite / 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 / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailsclosest to the average, model1
AuthorsSaponaro, A. / Pauleta, S.R. / Cantini, F. / Matzapetakis, M. / Hammann, C. / Banci, L. / Thiel, G. / Santoro, B. / Moroni, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for the mutual antagonism of cAMP and TRIP8b in regulating HCN channel function.
Authors: Saponaro, A. / Pauleta, S.R. / Cantini, F. / Matzapetakis, M. / Hammann, C. / Donadoni, C. / Hu, L. / Thiel, G. / Banci, L. / Santoro, B. / Moroni, A.
History
DepositionMay 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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 2


Theoretical massNumber of molelcules
Total (without water)17,9881
Polymers17,9881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / HCN2 / Brain cyclic nucleotide-gated channel 2 / BCNG-2


Mass: 17987.891 Da / Num. of mol.: 1
Fragment: cyclic nucleotide binding domain (UNP residues 521-672)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCN2, BCNG2 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9UL51

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D HNCO
1523D HN(CA)CB
1613D 1H-15N NOESY
1723D 1H-13C NOESY
1823D (H)CCH-TOCSY
1932D 1H-1H NOESY
11032D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-15N] HCN2 CNBD, 20 mM potassium phosphate, 150 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] HCN2 CNBD, 20 mM potassium phosphate, 150 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
31 mM HCN2 CNBD, 20 mM potassium phosphate, 150 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHCN2 CNBD-1[U-15N]1
20 mMpotassium phosphate-21
150 mMpotassium chloride-31
1 mMHCN2 CNBD-4[U-13C; U-15N]2
20 mMpotassium phosphate-52
150 mMpotassium chloride-62
1 mMHCN2 CNBD-73
20 mMpotassium phosphate-83
150 mMpotassium chloride-93
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.8Keller and Wuthrichchemical shift assignment
CARA1.8Keller and Wuthrichdata analysis
CARA1.8Keller and Wuthrichpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber12Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CINGGeerten Vuister, Jurgen F. Doreleijers and Alan Wilter Sousa da Silvastructure validation
PSVSBhattacharya and Montelionestructure validation
CANDIDHerrmann, Guntert and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1841 / NOE intraresidue total count: 508 / NOE long range total count: 461 / NOE medium range total count: 295 / NOE sequential total count: 577 / Hydrogen bond constraints total count: 36 / Protein phi angle constraints total count: 103 / Protein psi angle constraints total count: 103
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 14.91 ° / Maximum upper distance constraint violation: 0.38 Å

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