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- PDB-3u10: Tetramerization dynamics of the C-terminus underlies isoform-spec... -

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Basic information

Entry
Database: PDB / ID: 3u10
TitleTetramerization dynamics of the C-terminus underlies isoform-specific cAMP-gating in HCN channels
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


HCN channels / HCN channel complex / cellular response to cGMP / regulation of membrane depolarization / intracellularly cAMP-activated cation channel activity / membrane depolarization during cardiac muscle cell action potential / sodium ion import across plasma membrane / voltage-gated sodium channel activity / voltage-gated potassium channel activity / potassium ion import across plasma membrane ...HCN channels / HCN channel complex / cellular response to cGMP / regulation of membrane depolarization / intracellularly cAMP-activated cation channel activity / membrane depolarization during cardiac muscle cell action potential / sodium ion import across plasma membrane / voltage-gated sodium channel activity / voltage-gated potassium channel activity / potassium ion import across plasma membrane / sodium ion transmembrane transport / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / voltage-gated potassium channel complex / regulation of membrane potential / cell-cell signaling / axon / dendrite / identical protein binding / plasma membrane
Similarity search - Function
Helix hairpin bin / 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 ...Helix hairpin bin / 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 / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLolicato, M. / Nardini, M. / Gazzarrini, S. / Moller, S. / Bertinetti, D. / Herberg, F.W. / Bolognesi, M. / Martin, H. / Fasolini, M. / Bertrand, J.A. ...Lolicato, M. / Nardini, M. / Gazzarrini, S. / Moller, S. / Bertinetti, D. / Herberg, F.W. / Bolognesi, M. / Martin, H. / Fasolini, M. / Bertrand, J.A. / Arrigoni, C. / Thiel, G. / Moroni, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Tetramerization dynamics of C-terminal domain underlies isoform-specific cAMP gating in hyperpolarization-activated cyclic nucleotide-gated channels.
Authors: Lolicato, M. / Nardini, M. / Gazzarrini, S. / Moller, S. / Bertinetti, D. / Herberg, F.W. / Bolognesi, M. / Martin, H. / Fasolini, M. / Bertrand, J.A. / Arrigoni, C. / Thiel, G. / Moroni, A.
History
DepositionSep 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8602
Polymers24,5311
Non-polymers3291
Water1,54986
1
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4418
Polymers98,1254
Non-polymers1,3174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area11230 Å2
ΔGint-43 kcal/mol
Surface area40150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.730, 96.730, 50.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

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


Mass: 24531.143 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 470-672)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCN2, BCNG2 / Plasmid: pET-24 modified with the LIC cloning cassette / Production host: Escherichia coli (E. coli) / Strain (production host): K12 Rosetta codon plus / References: UniProt: Q9UL51
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 4.6
Details: 20% PEG 8000, 0.5M NaCl, 0.1M Citrate buffer (pH 4.6), 10% glycerol, VAPOR DIFFUSION, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 29, 2010
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.3→35.03 Å / Num. obs: 11143 / % possible obs: 99.8 % / Observed criterion σ(F): 14.3 / Observed criterion σ(I): 14.3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.128
Reflection shellResolution: 2.3→2.42 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q43

1q43


Resolution: 2.3→32.93 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.889 / SU B: 7.263 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 531 4.8 %RANDOM
Rwork0.20041 ---
obs0.20377 10592 99.49 %-
all-10592 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 22 86 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221713
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.9832303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37823.02386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30315317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2911516
X-RAY DIFFRACTIONr_chiral_restr0.1230.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211291
X-RAY DIFFRACTIONr_mcbond_it0.9891.51002
X-RAY DIFFRACTIONr_mcangle_it1.95121613
X-RAY DIFFRACTIONr_scbond_it3.4083711
X-RAY DIFFRACTIONr_scangle_it5.5084.5690
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 34 -
Rwork0.22 754 -
obs--100 %

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