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- PDB-5j7e: hEAG PAS domain -

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Basic information

Entry
Database: PDB / ID: 5j7e
TitlehEAG PAS domain
ComponentsPotassium voltage-gated channel subfamily H member 1
KeywordsTRANSPORT PROTEIN / KCNH channels / PAS domain / ether-a-go-go channel
Function / homology
Function and homology information


delayed rectifier potassium channel activity / Voltage gated Potassium channels / myoblast fusion / nuclear inner membrane / phosphatidylinositol bisphosphate binding / voltage-gated potassium channel complex / potassium ion transmembrane transport / cellular response to calcium ion / regulation of membrane potential / postsynaptic density membrane ...delayed rectifier potassium channel activity / Voltage gated Potassium channels / myoblast fusion / nuclear inner membrane / phosphatidylinositol bisphosphate binding / voltage-gated potassium channel complex / potassium ion transmembrane transport / cellular response to calcium ion / regulation of membrane potential / postsynaptic density membrane / potassium ion transport / regulation of cell population proliferation / presynaptic membrane / early endosome membrane / perikaryon / calmodulin binding / axon / intracellular membrane-bounded organelle / dendrite / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, EAG / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Cyclic nucleotide-monophosphate binding domain ...Potassium channel, voltage-dependent, EAG / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Beta-Lactamase / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Voltage-gated delayed rectifier potassium channel KCNH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsXue, T. / Juan, S. / Xiaohong, Q.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaNo.31400645 China
Natural Science Foundation of TianjinNo. 15JCQNJC09800 China
State Key Laboratory of Medicinal Chemical BiologyNo.20150629 China
CitationJournal: To Be Published
Title: Crystal Structure of PAS domain from the hEAG Potassium Channel
Authors: Xue, T. / Juan, S. / Xiaohong, Q.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _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 voltage-gated channel subfamily H member 1
B: Potassium voltage-gated channel subfamily H member 1
C: Potassium voltage-gated channel subfamily H member 1
D: Potassium voltage-gated channel subfamily H member 1
E: Potassium voltage-gated channel subfamily H member 1
F: Potassium voltage-gated channel subfamily H member 1


Theoretical massNumber of molelcules
Total (without water)101,6426
Polymers101,6426
Non-polymers00
Water00
1
A: Potassium voltage-gated channel subfamily H member 1


Theoretical massNumber of molelcules
Total (without water)16,9401
Polymers16,9401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Potassium voltage-gated channel subfamily H member 1


Theoretical massNumber of molelcules
Total (without water)16,9401
Polymers16,9401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Potassium voltage-gated channel subfamily H member 1


Theoretical massNumber of molelcules
Total (without water)16,9401
Polymers16,9401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Potassium voltage-gated channel subfamily H member 1


Theoretical massNumber of molelcules
Total (without water)16,9401
Polymers16,9401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Potassium voltage-gated channel subfamily H member 1


Theoretical massNumber of molelcules
Total (without water)16,9401
Polymers16,9401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Potassium voltage-gated channel subfamily H member 1


Theoretical massNumber of molelcules
Total (without water)16,9401
Polymers16,9401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)213.974, 39.058, 106.802
Angle α, β, γ (deg.)90.00, 118.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Potassium voltage-gated channel subfamily H member 1 / hEAG1 / h-eag / Ether-a-go-go potassium channel 1


Mass: 16940.350 Da / Num. of mol.: 6 / Fragment: PAS domain, UNP residues 1-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNH1, EAG, EAG1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpKan_Alpha_S (others)
References: UniProt: O95259

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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: 1.94 Å3/Da / Density % sol: 36.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20 mM Tris-HCl, 200 mM NaCl, 5 mM DTT

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 59648 / % possible obs: 96.36 % / Redundancy: 1.7 % / Biso Wilson estimate: 16 Å2 / Net I/σ(I): 4.14
Reflection shellResolution: 1.905→1.973 Å

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z6C

2z6c


Resolution: 1.9→29.13 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 217422.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.231 5859 10.1 %RANDOM
Rwork0.214 ---
obs0.214 57859 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.2473 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å20 Å2-1.32 Å2
2--6.52 Å20 Å2
3----4.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 0 0 383 5744
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.712.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 798 10.3 %
Rwork0.245 6957 -
obs--75.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top

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