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- PDB-1q3e: HCN2J 443-645 in the presence of cGMP -

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Basic information

Entry
Database: PDB / ID: 1q3e
TitleHCN2J 443-645 in the presence of cGMP
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
KeywordsTRANSPORT PROTEIN / CNBD / C-LINKER / PACEMAKER / HCN / CHANNEL / CYCLIC NUCLEOTIDE / CAP / PKA / cGMP / ION CHANNEL / LIGAND
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 / dendritic shaft / regulation of membrane potential / 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
CYCLIC GUANOSINE 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: 1.9 Å
AuthorsZagotta, W.N. / Olivier, N.B. / Black, K.D. / Young, E.C. / Olson, R. / Gouaux, J.E.
CitationJournal: Nature / Year: 2003
Title: Structural basis for modulation and agonist specificity of HCN pacemaker channels
Authors: Zagotta, W.N. / Olivier, N.B. / Black, K.D. / Young, E.C. / Olson, R. / Gouaux, J.E.
History
DepositionJul 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

Downloads & links

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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)49,0764
Polymers48,3862
Non-polymers6902
Water5,945330
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)98,1528
Polymers96,7714
Non-polymers1,3814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area11310 Å2
ΔGint-55 kcal/mol
Surface area35600 Å2
MethodPISA
2
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)98,1528
Polymers96,7714
Non-polymers1,3814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area11280 Å2
ΔGint-54 kcal/mol
Surface area34510 Å2
MethodPISA
3
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

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)196,30416
Polymers193,5428
Non-polymers2,7628
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area27140 Å2
ΔGint-148 kcal/mol
Surface area65560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.236, 94.236, 124.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a tetramer generated from the one protmer. There are two distinct protomers in the asymmetric unit labeled A & B. Each protomer associates with its like to form the tetramer. To generate the tetramer apply the following symmetry operations to the asymmetric unit: 1-y,x,z and y,1-x,z and 1-x,1-y,z

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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: 24192.781 Da / Num. of mol.: 2 / Fragment: Residues 443-645 (Reference sequence numbering)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: HCN2 OR BCNG2 OR HAC1 / Organ: brain / Plasmid: pETGQ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: O88703
#2: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE / Cyclic guanosine monophosphate


Mass: 345.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 400, sodium citrate, sodium chloride, DTT, HEPES, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1200 mM1reservoirNaCl
2100 mMcitrate1reservoirpH4.6
315 %PEG4001reservoir
42.3 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 19, 2002
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→29.35 Å / Num. all: 41314 / Num. obs: 41314 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 35.3 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 31.1
Reflection shellResolution: 1.9→2.02 Å / Rmerge(I) obs: 0.242 / % possible all: 85
Reflection
*PLUS

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.35 Å
Isotropic thermal model: overall b-value correction. B-factor correction applied to coordinate array B: -0.640
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Model of ligand omitted until R-work below 30%.
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 4164 -random
Rwork0.2099 ---
all-41314 --
obs-41314 97.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.667 Å20 Å20 Å2
2--2.667 Å20 Å2
3----5.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3011 0 46 330 3387
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006486
X-RAY DIFFRACTIONc_angle_deg1.19396
X-RAY DIFFRACTIONc_dihedral_angle_d21.77128
X-RAY DIFFRACTIONc_improper_angle_d0.77036
X-RAY DIFFRACTIONc_mcangle_it1.8892
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_scbond_it2.1882
X-RAY DIFFRACTIONc_scangle_it3.1042.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.279 619 -
Rwork0.242 --
obs-5393 85 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2DRGCNS.PARAM
X-RAY DIFFRACTION3water.param
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.77128
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77036

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