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- PDB-4f8a: Cyclic nucleotide binding-homology domain from mouse EAG1 potassi... -

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Basic information

Entry
Database: PDB / ID: 4f8a
TitleCyclic nucleotide binding-homology domain from mouse EAG1 potassium channel
ComponentsPotassium voltage-gated channel subfamily H member 1
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / probable regulatory domain of potassium channel
Function / homology
Function and homology information


Voltage gated Potassium channels / potassium channel complex / regulation of presynaptic cytosolic calcium ion concentration / delayed rectifier potassium channel activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / parallel fiber to Purkinje cell synapse / nuclear inner membrane / phosphatidylinositol bisphosphate binding / regulation of synaptic vesicle exocytosis / startle response ...Voltage gated Potassium channels / potassium channel complex / regulation of presynaptic cytosolic calcium ion concentration / delayed rectifier potassium channel activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / parallel fiber to Purkinje cell synapse / nuclear inner membrane / phosphatidylinositol bisphosphate binding / regulation of synaptic vesicle exocytosis / startle response / axolemma / voltage-gated potassium channel complex / potassium ion transmembrane transport / cellular response to calcium ion / monoatomic ion transmembrane transport / regulation of membrane potential / 14-3-3 protein binding / postsynaptic density membrane / presynaptic membrane / regulation of cell population proliferation / perikaryon / early endosome membrane / transmembrane transporter binding / calmodulin binding / axon / intracellular membrane-bounded organelle / neuronal cell body / dendrite / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, EAG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAS domain / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...Potassium channel, voltage-dependent, EAG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAS domain / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / 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 / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily H member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMarques-Carvalho, M.J. / Sahoo, N. / Muskett, F.W. / Vieira-Pires, R.S. / Gabant, G. / Cadene, M. / Schonherr, R. / Morais-Cabral, J.H.
Citation
Journal: J.Mol.Biol. / Year: 2012
Title: Structural, Biochemical, and Functional Characterization of the Cyclic Nucleotide Binding Homology Domain from the Mouse EAG1 Potassium Channel.
Authors: Marques-Carvalho, M.J. / Sahoo, N. / Muskett, F.W. / Vieira-Pires, R.S. / Gabant, G. / Cadene, M. / Schonherr, R. / Morais-Cabral, J.H.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystallization and preliminary X-ray crystallographic characterization of a cyclic nucleotide-binding homology domain from the mouse EAG potassium channel.
Authors: Marques-Carvalho, M.J. / Morais-Cabral, J.H.
History
DepositionMay 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily H member 1


Theoretical massNumber of molelcules
Total (without water)18,0201
Polymers18,0201
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.346, 60.346, 85.415
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Potassium voltage-gated channel subfamily H member 1 / Ether-a-go-go potassium channel 1 / EAG channel 1 / EAG1 / m-eag / Voltage-gated potassium channel ...Ether-a-go-go potassium channel 1 / EAG channel 1 / EAG1 / m-eag / Voltage-gated potassium channel subunit Kv10.1


Mass: 18019.867 Da / Num. of mol.: 1
Fragment: Cyclic nucleotide binding-homology domain (unp residues 552-707)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eag, Kcnh1 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60603
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.2 M tri-sodium citrate di-hydrate, 20% (w/v) PEG 3350, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.2→52.3 Å / Num. all: 9566 / Num. obs: 9566 / % possible obs: 99.4 % / Observed criterion σ(F): 1.37 / Observed criterion σ(I): 2.2 / Biso Wilson estimate: 44.53 Å2 / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.2→2.31 Å / Rmerge(I) obs: 0.251 / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→52.261 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8415 / SU ML: 0.45 / σ(F): 1.37 / Phase error: 22.04 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 459 4.81 %5%
Rwork0.1892 ---
obs0.1907 9538 99.41 %-
all-9566 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.948 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 137.08 Å2 / Biso mean: 58.2904 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.9636 Å2-0 Å20 Å2
2--1.9636 Å2-0 Å2
3----3.9272 Å2
Refinement stepCycle: LAST / Resolution: 2.2→52.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 0 41 1197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081191
X-RAY DIFFRACTIONf_angle_d1.1091613
X-RAY DIFFRACTIONf_chiral_restr0.081183
X-RAY DIFFRACTIONf_plane_restr0.004208
X-RAY DIFFRACTIONf_dihedral_angle_d12.66425
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.33772.0166-2.6430.6422-0.79433.36290.27980.9459-0.5816-1.6441-0.1736-2.71021.0754-0.32560.4210.5945-0.03470.22730.7892-0.31940.78856.282318.864-28.2596
23.41240.4864-1.93253.10781.03167.1927-0.07020.28310.6459-0.0630.56180.1217-0.4478-0.0032-0.44190.1754-0.01540.02760.55570.02630.3624-3.877925.9581-18.7479
36.33735.6379-0.24475.0610.19563.647-0.67460.7521-0.1627-0.56410.657-0.92170.10331.0301-0.11180.01920.04250.03810.7121-0.08390.38033.094120.0661-18.1057
43.69261.81360.11873.87070.46317.2203-0.07850.5014-0.7980.72530.1084-0.06460.77990.49880.0790.42890.0160.0870.49650.0530.4082-15.22138.3445-14.4609
55.85620.2843-1.56972.36161.34276.41930.0035-0.21950.17340.3804-0.00040.5730.9475-0.15830.12360.1247-0.04620.17670.34320.19310.4754-17.329614.8597-11.3298
63.66254.1628-0.75996.43870.99023.87840.513-0.80510.55290.9722-0.36610.90340.34180.1105-0.12590.3637-0.02840.17780.5012-0.05420.4088-14.875517.4622-6.0829
73.74-1.15962.13953.8232-2.61096.9467-0.127-0.05680.52530.4892-0.23610.09090.3850.25920.23380.4492-0.13420.15040.50640.09750.3942-18.048310.1927-9.9499
83.57082.3942-0.12272.69420.75791.61180.0058-0.88410.08980.60040.2824-0.36090.22621.3333-0.14180.17460.1576-0.14091.0461-0.09250.23820.723817.9495-10.1574
98.09624.3645-1.69179.54511.33746.44980.7323-1.57121.29980.587-0.53360.27470.33641.17170.01260.40850.040.19190.6079-0.22970.4791-8.684722.6561-3.9241
105.15183.22320.09785.25941.65973.2877-0.2849-0.7493-0.66290.594-0.7340.8410.9069-1.1479-0.57911.2875-0.15760.53930.996-0.13620.6624-23.15314.04343.3574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 562:566)A562 - 566
2X-RAY DIFFRACTION2(chain A and resid 567:586)A567 - 586
3X-RAY DIFFRACTION3(chain A and resid 587:597)A587 - 597
4X-RAY DIFFRACTION4(chain A and resid 598:615)A598 - 615
5X-RAY DIFFRACTION5(chain A and resid 616:631)A616 - 631
6X-RAY DIFFRACTION6(chain A and resid 632:652)A632 - 652
7X-RAY DIFFRACTION7(chain A and resid 653:667)A653 - 667
8X-RAY DIFFRACTION8(chain A and resid 668:688)A668 - 688
9X-RAY DIFFRACTION9(chain A and resid 689:702)A689 - 702
10X-RAY DIFFRACTION10(chain A and resid 703:707)A703 - 707

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