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- PDB-5khh: HCN2 CNBD in complex with inosine-3', 5'-cyclic monophosphate (cIMP) -

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Basic information

Entry
Database: PDB / ID: 5khh
TitleHCN2 CNBD in complex with inosine-3', 5'-cyclic monophosphate (cIMP)
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
KeywordsTRANSPORT PROTEIN / protein-ligand complex / cycilc nucleotide binding domain / ion transport
Function / homology
Function and homology information


HCN channels / HCN channel complex / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / sodium ion import across plasma membrane / voltage-gated sodium channel activity / regulation of membrane depolarization / potassium ion import across plasma membrane / voltage-gated potassium channel activity / sodium ion transmembrane transport ...HCN channels / HCN channel complex / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / sodium ion import across plasma membrane / voltage-gated sodium channel activity / regulation of membrane depolarization / potassium ion import across plasma membrane / voltage-gated potassium channel activity / sodium ion transmembrane transport / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / somatodendritic compartment / dendrite membrane / regulation of membrane potential / dendritic shaft / PDZ domain binding / molecular adaptor activity / axon / neuronal cell body / dendrite / protein-containing complex binding / membrane / 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
Inosine-3',5'-cyclic monophosphate / Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsNg, L.C.T. / Putrenko, I. / Baronas, V. / Van Petegem, F. / Accili, E.A.
CitationJournal: Structure / Year: 2016
Title: Cyclic Purine and Pyrimidine Nucleotides Bind to the HCN2 Ion Channel and Variably Promote C-Terminal Domain Interactions and Opening.
Authors: Ng, L.C. / Putrenko, I. / Baronas, V. / Van Petegem, F. / Accili, E.A.
History
DepositionJun 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)24,2142
Polymers23,8831
Non-polymers3301
Water2,972165
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)96,8548
Polymers95,5334
Non-polymers1,3214
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 area9120 Å2
ΔGint-50 kcal/mol
Surface area36150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.037, 96.037, 115.913
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 23883.330 Da / Num. of mol.: 1 / Fragment: UNP residues 443-643
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hcn2, Bcng2, Hac1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O88703
#2: Chemical ChemComp-6SW / Inosine-3',5'-cyclic monophosphate / cIMP


Mass: 330.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11N4O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 200 mM NaCl, 0.1 mM sodium citrate pH 5.5, 14.5% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97944 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2012 / Details: 1000 um thick sensor
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 1.77→44.12 Å / Num. obs: 26044 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 9.83 % / Biso Wilson estimate: 42.756 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.06
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.77-1.881.1472.1195.2
1.88-2.010.5285.07196.5
2.01-2.170.23710.41197.6
2.17-2.370.13217.14197.3
2.37-2.650.08224.51198.2
2.65-3.060.0632.07198.5
3.06-3.740.0538.12199
3.74-5.270.05840.86199.3
5.27-44.0470.06639.23198.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q5O

1q5o


Resolution: 1.77→44.12 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.738 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.13 / Details: molecular replacement
RfactorNum. reflection% reflectionSelection details
Rfree0.2628 1301 5.1 %RANDOM
Rwork0.2144 ---
obs0.2167 24442 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.67 Å2 / Biso mean: 36.579 Å2 / Biso min: 21.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.77→44.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1571 0 22 166 1759
Biso mean--33.65 44.86 -
Num. residues----195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191680
X-RAY DIFFRACTIONr_bond_other_d0.0010.021554
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9782277
X-RAY DIFFRACTIONr_angle_other_deg0.79233566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8425206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39823.01283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99715288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6711515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021926
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02415
LS refinement shellResolution: 1.771→1.817 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 94 -
Rwork0.421 1711 -
all-1805 -
obs--92.99 %

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