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- PDB-5khi: HCN2 CNBD in complex with purine riboside-3', 5'-cyclic monophosp... -

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Basic information

Entry
Database: PDB / ID: 5khi
TitleHCN2 CNBD in complex with purine riboside-3', 5'-cyclic monophosphate (cPuMP)
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 / cellular response to aldosterone / HCN channel complex / ammonium transmembrane transport / cellular response to cGMP / intracellularly cAMP-activated cation channel activity / sodium ion import across plasma membrane / voltage-gated sodium channel activity / potassium ion import across plasma membrane / voltage-gated potassium channel activity ...HCN channels / cellular response to aldosterone / HCN channel complex / ammonium transmembrane transport / cellular response to cGMP / intracellularly cAMP-activated cation channel activity / sodium ion import across plasma membrane / voltage-gated sodium channel activity / potassium ion import across plasma membrane / voltage-gated potassium channel activity / cAMP binding / potassium ion transmembrane transport / dendrite membrane / cellular response to cAMP / dendritic shaft / regulation of membrane potential / PDZ domain binding / molecular adaptor activity / response to xenobiotic stimulus / axon / neuronal cell body / protein-containing complex binding / identical protein binding / membrane / 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
Purine riboside-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: 2.1 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)24,1982
Polymers23,8831
Non-polymers3141
Water70339
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)96,7908
Polymers95,5334
Non-polymers1,2574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area8680 Å2
ΔGint-44 kcal/mol
Surface area37620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.278, 96.278, 46.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / 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-6SX / Purine riboside-3',5'-cyclic monophosphate / cPuMP


Mass: 314.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11N4O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 200 mM NaCl, 0.1 mM sodium citrate pH 5.5, 18% 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: 2.1→31.7 Å / Num. obs: 13266 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.04 % / Biso Wilson estimate: 54.763 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.6
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.230.8282.68199
2.23-2.380.4684.77199.9
2.38-2.570.277.961100
2.57-2.820.14213.71199.9
2.82-3.150.07522.12199.8
3.15-3.630.04832.65199.6
3.63-4.440.03741.24199.6
4.44-6.250.03643.11199.3
6.25-48.0710.0541.38197.3

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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: 2.1→31.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.522 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.196 / Details: molecular replacement
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 648 4.9 %RANDOM
Rwork0.2006 ---
obs0.2029 12541 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.62 Å2 / Biso mean: 58.676 Å2 / Biso min: 35.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 2.1→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 21 39 1683
Biso mean--54.83 53.68 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191680
X-RAY DIFFRACTIONr_bond_other_d0.0010.021570
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9792265
X-RAY DIFFRACTIONr_angle_other_deg0.74833595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5725200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53822.85784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26515292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8341516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021890
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 51 -
Rwork0.287 890 -
all-941 -
obs--99.16 %

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