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- PDB-5khj: HCN2 CNBD in complex with uridine-3', 5'-cyclic monophosphate (cUMP) -

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Basic information

Entry
Database: PDB / ID: 5khj
TitleHCN2 CNBD in complex with uridine-3', 5'-cyclic monophosphate (cUMP)
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 / sodium ion import across plasma membrane / voltage-gated sodium channel activity / potassium ion import across plasma membrane / voltage-gated potassium channel activity / cAMP binding ...HCN channels / HCN channel complex / ammonium transmembrane transport / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / sodium ion import across plasma membrane / voltage-gated sodium channel activity / potassium ion import across plasma membrane / voltage-gated potassium channel activity / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / regulation of membrane potential / 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
Uridine-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: 2.01 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
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3474
Polymers47,7352
Non-polymers6122
Water5,657314
1
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6948
Polymers95,4694
Non-polymers1,2254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area8620 Å2
ΔGint-37 kcal/mol
Surface area36590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.486, 89.925, 98.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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: 23867.330 Da / Num. of mol.: 2 / 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-6SY / Uridine-3',5'-cyclic monophosphate / cUMP


Mass: 306.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.18 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 200 mM NaCl, 0.1 mM sodium citrate pH 4.6, 13% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2012 / Details: 1000 um thick sensor
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.01→28.69 Å / Num. obs: 27507 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 1.54 % / Biso Wilson estimate: 36.11 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.063 / Net I/σ(I): 7.35
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.01-2.130.3532194.3
2.13-2.280.2283.05199
2.28-2.460.1664.15198.4
2.46-2.690.1235.57197.6
2.69-3.010.088.35195.7
3.01-3.460.05612.19192.8
3.46-4.230.04615.38190.8
4.23-5.910.03816.7189.5
5.91-28.6750.03617.2186.1

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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: 2.01→28.69 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.778 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.191 / Details: molecular replacement
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 1395 5.1 %RANDOM
Rwork0.1814 ---
obs0.185 26112 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.97 Å2 / Biso mean: 32.349 Å2 / Biso min: 15.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å2-0 Å2
2--0.29 Å2-0 Å2
3---0.57 Å2
Refinement stepCycle: final / Resolution: 2.01→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 40 314 3514
Biso mean--26.64 42.88 -
Num. residues----400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193274
X-RAY DIFFRACTIONr_bond_other_d0.0010.023040
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9734420
X-RAY DIFFRACTIONr_angle_other_deg0.87236947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.78922.68153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46115553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5121528
X-RAY DIFFRACTIONr_chiral_restr0.10.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023709
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02815
LS refinement shellResolution: 2.009→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 77 -
Rwork0.212 1771 -
all-1848 -
obs--90.59 %

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