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- PDB-5khg: HCN2 CNBD in complex with cytidine-3', 5'-cyclic monophosphate (cCMP) -

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Basic information

Entry
Database: PDB / ID: 5khg
TitleHCN2 CNBD in complex with cytidine-3', 5'-cyclic monophosphate (cCMP)
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 / ammonium transmembrane transport / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / regulation of membrane depolarization / sodium ion import across plasma membrane / voltage-gated sodium channel activity / potassium ion import across plasma membrane / voltage-gated potassium channel activity ...HCN channels / HCN channel complex / ammonium transmembrane transport / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / regulation of membrane depolarization / sodium ion import across plasma membrane / voltage-gated sodium channel activity / potassium ion import across plasma membrane / voltage-gated potassium channel activity / sodium ion transmembrane transport / cAMP binding / cellular response to cAMP / somatodendritic compartment / dendrite membrane / potassium ion transmembrane transport / regulation of membrane potential / dendritic shaft / PDZ domain binding / molecular adaptor activity / axon / neuronal cell body / dendrite / 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
Chem-CC7 / Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.241 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)24,1892
Polymers23,8831
Non-polymers3051
Water46826
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)96,7548
Polymers95,5334
Non-polymers1,2214
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 area8640 Å2
ΔGint-42 kcal/mol
Surface area37290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.204, 96.204, 46.680
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-CC7 / 4-amino-1-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxidotetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]pyrimidin-2(1H)-one


Mass: 305.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N3O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 200 mM NaCl, 0.1 mM sodium citrate pH 5.0, 16% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 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: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.23→30.422 Å / Num. obs: 10939 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 60.17 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.095 / Χ2: 1 / Net I/σ(I): 10.85 / Num. measured all: 58427
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.23-2.370.9921.958686172216570.7241.10196.2
2.37-2.530.5543.559058166316580.9040.61499.7
2.53-2.730.3395.738397153915310.950.37699.5
2.73-2.990.1839.317672141514090.9810.20399.6
2.99-3.350.10314.117045131113050.9910.11499.5
3.35-3.860.07918.826074114811420.9920.08799.5
3.86-4.720.06821.3352149989840.9910.07598.6
4.72-6.650.06621.6540898007830.990.07397.9
6.65-48.0490.07921.0121925004700.9890.08894

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1Q5O

1q5o


Resolution: 2.241→30.422 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.81 / Stereochemistry target values: ML / Details: molecular replacement
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 506 4.8 %RANDOM
Rwork0.2231 10045 --
obs0.2252 10551 95.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.87 Å2 / Biso mean: 66.8621 Å2 / Biso min: 40.84 Å2
Refinement stepCycle: final / Resolution: 2.241→30.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 20 26 1645
Biso mean--68.88 59.67 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081654
X-RAY DIFFRACTIONf_angle_d1.0062233
X-RAY DIFFRACTIONf_chiral_restr0.051240
X-RAY DIFFRACTIONf_plane_restr0.006288
X-RAY DIFFRACTIONf_dihedral_angle_d14.517979
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.241-2.46640.34891260.28862370249693
2.4664-2.82310.35691380.282532267099
2.8231-3.55590.27381250.26182572269799
3.5559-30.42520.23441170.19292571268893

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