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- PDB-3u0z: Tetramerization dynamics of the C-terminus underlies isoform-spec... -

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Basic information

Entry
Database: PDB / ID: 3u0z
TitleTetramerization dynamics of the C-terminus underlies isoform-specific cAMP-gating in HCN channels
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
KeywordsTRANSPORT PROTEIN / helix / beta sheet / cNMP binding
Function / homology
Function and homology information


HCN channels / regulation of membrane hyperpolarization / HCN channel complex / retinal cone cell development / : / intracellularly cAMP-activated cation channel activity / positive regulation of cation channel activity / negative regulation of action potential / apical dendrite / apical protein localization ...HCN channels / regulation of membrane hyperpolarization / HCN channel complex / retinal cone cell development / : / intracellularly cAMP-activated cation channel activity / positive regulation of cation channel activity / negative regulation of action potential / apical dendrite / apical protein localization / voltage-gated monoatomic cation channel activity / voltage-gated sodium channel activity / regulation of membrane depolarization / voltage-gated potassium channel activity / plasma membrane => GO:0005886 / phosphatidylinositol-3,4,5-trisphosphate binding / sodium ion transmembrane transport / axon terminus / cAMP binding / cellular response to cAMP / somatodendritic compartment / potassium ion transmembrane transport / dendrite membrane / phosphatidylinositol-4,5-bisphosphate binding / regulation of membrane potential / dendritic shaft / response to calcium ion / protein homotetramerization / basolateral plasma membrane / axon / dendrite / neuronal cell body / synapse / protein-containing complex binding / cell surface / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1 / 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. ...Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1 / 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 / Voltage-dependent channel 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 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLolicato, M. / Nardini, M. / Gazzarrini, S. / Moller, S. / Bertinetti, D. / Herberg, F.W. / Bolognesi, M. / Martin, H. / Fasolini, M. / Bertrand, J.A. ...Lolicato, M. / Nardini, M. / Gazzarrini, S. / Moller, S. / Bertinetti, D. / Herberg, F.W. / Bolognesi, M. / Martin, H. / Fasolini, M. / Bertrand, J.A. / Arrigoni, C. / Thiel, G. / Moroni, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Tetramerization dynamics of C-terminal domain underlies isoform-specific cAMP gating in hyperpolarization-activated cyclic nucleotide-gated channels.
Authors: Lolicato, M. / Nardini, M. / Gazzarrini, S. / Moller, S. / Bertinetti, D. / Herberg, F.W. / Bolognesi, M. / Martin, H. / Fasolini, M. / Bertrand, J.A. / Arrigoni, C. / Thiel, G. / Moroni, A.
History
DepositionSep 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 1, 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 / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 1
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7214
Polymers49,0622
Non-polymers6582
Water88349
1
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4418
Polymers98,1244
Non-polymers1,3174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area11250 Å2
ΔGint-35 kcal/mol
Surface area40580 Å2
MethodPISA
2
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4418
Polymers98,1244
Non-polymers1,3174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area11280 Å2
ΔGint-35 kcal/mol
Surface area40620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.670, 97.670, 113.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 390 - 588 / Label seq-ID: 8 - 206

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1 / Brain cyclic nucleotide-gated channel 1 / BCNG-1 / Hyperpolarization-activated cation channel 2 / HAC-2


Mass: 24531.117 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 390-592)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hcn1, Bcng1, Hac2 / Plasmid: modified pET-24 with LIC cloning cassette / Production host: Escherichia coli (E. coli) / Strain (production host): K12 Rosetta codon plus / References: UniProt: O88704
#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.: 49 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 5
Details: 20-22% PEG 3350, 0.4M Sodium Acetate buffer (pH 5.0), VAPOR DIFFUSION, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97238 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2010
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97238 Å / Relative weight: 1
ReflectionResolution: 2.9→43.78 Å / Num. obs: 11821 / % possible obs: 100 % / Observed criterion σ(F): 12.5 / Observed criterion σ(I): 12.5 / Redundancy: 6.6 % / Rmerge(I) obs: 0.12
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.485 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q43

1q43


Resolution: 2.9→43.78 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.857 / SU B: 16.696 / SU ML: 0.312 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27497 560 4.7 %RANDOM
Rwork0.20496 ---
all0.20812 ---
obs0.20812 11258 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.646 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.9→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 44 49 3371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223399
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9784570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1785397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04223.22177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.15115632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.41533
X-RAY DIFFRACTIONr_chiral_restr0.1120.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212573
X-RAY DIFFRACTIONr_mcbond_it0.6581.51981
X-RAY DIFFRACTIONr_mcangle_it1.35923195
X-RAY DIFFRACTIONr_scbond_it2.00431418
X-RAY DIFFRACTIONr_scangle_it3.4924.51374
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
794tight positional0.020.05
836medium positional0.030.5
794tight thermal0.170.5
836medium thermal0.222
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 47 -
Rwork0.3 828 -
obs--100 %

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