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- PDB-3etq: X-ray structure of cysteine-free fragment of mHCN2 C-terminal reg... -

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Basic information

Entry
Database: PDB / ID: 3etq
TitleX-ray structure of cysteine-free fragment of mHCN2 C-terminal region from amino acids 443-630 including C508N, C584S, and C601S mutations
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
KeywordsTRANSPORT PROTEIN / HCN / ion channel / cAMP / Cyclic nucleotide binding domain / beta roll / C-linker / cAMP-binding / Glycoprotein / Ion transport / Ionic channel / Membrane / Nucleotide-binding / Phosphoprotein / Potassium / Potassium channel / Potassium transport / Sodium / Sodium channel / Sodium transport / Transmembrane / Transport / Voltage-gated channel
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 / somatodendritic compartment / potassium ion transmembrane transport / dendrite membrane / regulation of membrane potential / dendritic shaft / PDZ domain binding / molecular adaptor activity / axon / dendrite / neuronal cell body / 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
ADENOSINE-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 / molecular replacement / Resolution: 1.9 Å
AuthorsFlynn, G.E.
CitationJournal: Nat.Methods / Year: 2009
Title: Mapping the structure and conformational movements of proteins with transition metal ion FRET.
Authors: Taraska, J.W. / Puljung, M.C. / Olivier, N.B. / Flynn, G.E. / Zagotta, W.N.
History
DepositionOct 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)48,4014
Polymers47,7422
Non-polymers6582
Water9,746541
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

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)193,60416
Polymers190,9708
Non-polymers2,6348
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
Buried area27130 Å2
ΔGint-146 kcal/mol
Surface area66990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.752, 95.752, 115.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-837-

HOH

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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: 23871.236 Da / Num. of mol.: 2 / Fragment: C-terminal fragment / Mutation: C508N, C584S, C601S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcng2, Hac1, Hcn2 / Plasmid: pMalc2T / Production host: Escherichia coli (E. coli) / Strain (production host): Bl-21 (DE3) / References: UniProt: O88703
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.77 Å3/Da / Density % sol: 55.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 16% w/v PEG 6000, 500 mM NaCl, 10% glycerol, 100 mM citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2004
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 42653 / % possible obs: 99.5 % / Redundancy: 27.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 66.615
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 19.6 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 8.6 / % possible all: 95.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å14.98 Å
Translation2.8 Å14.98 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1q5o

1q5o


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.348 / SU ML: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.216 2149 5 %
Rwork0.182 --
obs0.183 42629 99.5 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 21.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 44 541 3746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223291
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8641.9734469
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36623.471170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4715556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.521526
X-RAY DIFFRACTIONr_chiral_restr0.0670.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022547
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.21473
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22289
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.280.2392
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2990.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0551.52007
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64823138
X-RAY DIFFRACTIONr_scbond_it2.74431470
X-RAY DIFFRACTIONr_scangle_it4.0134.51319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å
RfactorNum. reflection% reflection
Rfree0.27 140 -
Rwork0.192 2772 -
obs--93.94 %

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