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- PDB-3u11: Tetramerization dynamics of the C-terminus underlies isoform-spec... -

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Basic information

Entry
Database: PDB / ID: 3u11
TitleTetramerization dynamics of the C-terminus underlies isoform-specific cAMP-gating in HCN channels
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
KeywordsTRANSPORT 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 SA node cell action potential ...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 SA node cell action potential / 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 / cAMP binding / potassium ion transmembrane transport / sodium ion transmembrane transport / muscle contraction / regulation of heart rate / cellular response to cAMP / regulation of membrane potential / axon / dendrite / perinuclear region of cytoplasm / 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. ...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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3719
Polymers49,2522
Non-polymers1,1197
Water2,648147
1
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,66328
Polymers98,5054
Non-polymers3,15924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15440 Å2
ΔGint-43 kcal/mol
Surface area38160 Å2
MethodPISA
2
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8218
Polymers98,5054
Non-polymers1,3174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area11790 Å2
ΔGint-45 kcal/mol
Surface area39260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.310, 88.310, 57.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

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


Mass: 24626.133 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 521-723)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCN4 / Plasmid: pET-24 modified with the LIC cloning cassette / Production host: Escherichia coli (E. coli) / Strain (production host): K12 Rosetta codon plus / References: UniProt: Q9Y3Q4
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 5
Details: 25% PEG 3350, 0.4M Sodium Acetate buffer, pH 5.0, 0.5M dibasic Ammonium phosphate, VAPOR DIFFUSION, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97238 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2010
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97238 Å / Relative weight: 1
ReflectionResolution: 2.5→62.44 Å / Num. obs: 15615 / % possible obs: 100 % / Observed criterion σ(F): 10 / Observed criterion σ(I): 10 / Redundancy: 4.8 % / Rmerge(I) obs: 0.132
Reflection shellResolution: 2.5→2.64 Å / % possible all: 100

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Processing

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

1q43


Resolution: 2.5→62.44 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.85 / SU B: 11.496 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27737 781 5 %RANDOM
Rwork0.19306 ---
all0.19727 14834 --
obs0.19727 14834 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.282 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.5→62.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 74 147 3531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223495
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9914697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.2985.098410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72722.637182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16415643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4521540
X-RAY DIFFRACTIONr_chiral_restr0.1320.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212636
X-RAY DIFFRACTIONr_mcbond_it0.7381.52005
X-RAY DIFFRACTIONr_mcangle_it1.44523246
X-RAY DIFFRACTIONr_scbond_it2.30131490
X-RAY DIFFRACTIONr_scangle_it3.8224.51448
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 57 -
Rwork0.255 1087 -
obs--100 %

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