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- PDB-4nvp: Structure of the cyclic nucleotide-binding domain of HCN4 channel... -

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Basic information

Entry
Database: PDB / ID: 4nvp
TitleStructure of the cyclic nucleotide-binding domain of HCN4 channel complexed with 7-CH-cAMP
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
KeywordsTRANSPORT PROTEIN / cyclic nucleotide binding domain / Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel / cytoplasmic domain
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 / voltage-gated sodium channel activity / blood circulation / regulation of membrane depolarization / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / 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
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
Chem-7CH / 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
AuthorsAlfieri, A. / Moroni, A.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Cyclic Nucleotide Mapping of Hyperpolarization-Activated Cyclic Nucleotide-Gated (HCN) Channels.
Authors: Moller, S. / Alfieri, A. / Bertinetti, D. / Aquila, M. / Schwede, F. / Lolicato, M. / Rehmann, H. / Moroni, A. / Herberg, F.W.
History
DepositionDec 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Apr 3, 2024Group: 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8262
Polymers24,4981
Non-polymers3281
Water66737
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)99,3058
Polymers97,9924
Non-polymers1,3134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area8990 Å2
ΔGint-35 kcal/mol
Surface area39160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.010, 96.010, 50.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-934-

HOH

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Components

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


Mass: 24498.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCN4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y3Q4
#2: Chemical ChemComp-7CH / (2S,4aR,6R,7R,7aS)-6-(4-amino-7H-pyrrolo[2,3-d]pyrimidin-7-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-oxide / 7-CH-cAMP


Mass: 328.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N4O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: HCN4 521-723 (10 mg mL-1) and 7-CH-cAMP 0.5mM were mixed in a 2:1 ratio with 100 mM TrisCl pH 8.0, 20 % PEG4000 (w/v), VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2013 / Details: bending magnet; bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97372 Å / Relative weight: 1
ReflectionResolution: 2.5→50.17 Å / Num. all: 8568 / Num. obs: 8568 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 8.1 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1215 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U11_A

Resolution: 2.5→44.47 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.961 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.604 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27031 406 4.8 %RANDOM
Rwork0.19799 ---
obs0.20117 8141 99.92 %-
all-8148 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.441 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0 Å2
2---0.05 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 22 37 1720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191738
X-RAY DIFFRACTIONr_bond_other_d0.0010.021635
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9812343
X-RAY DIFFRACTIONr_angle_other_deg0.7833762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.325204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17622.85791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.84215318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7571518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021942
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_mcbond_it2.8073.983807
X-RAY DIFFRACTIONr_mcbond_other2.7863.979806
X-RAY DIFFRACTIONr_mcangle_it4.425.9621008
X-RAY DIFFRACTIONr_mcangle_other4.4215.9691009
X-RAY DIFFRACTIONr_scbond_it3.64.376931
X-RAY DIFFRACTIONr_scbond_other3.5984.375932
X-RAY DIFFRACTIONr_scangle_other5.8146.3491334
X-RAY DIFFRACTIONr_long_range_B_refined8.00330.8041929
X-RAY DIFFRACTIONr_long_range_B_other8.00130.8041930
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 41 -
Rwork0.285 570 -
obs--99.67 %

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