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- PDB-4hqa: Crystal structure of PAS domain from the human ERG (hERG) potassi... -

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Basic information

Entry
Database: PDB / ID: 4hqa
TitleCrystal structure of PAS domain from the human ERG (hERG) potassium channel
ComponentsPotassium voltage-gated channel subfamily H member 2
KeywordsTRANSPORT PROTEIN / Potassium channel domain / PAS domain
Function / homology
Function and homology information


inward rectifier potassium channel complex / negative regulation of potassium ion export across plasma membrane / regulation of heart rate by hormone / Phase 3 - rapid repolarisation / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / negative regulation of potassium ion transmembrane transport / membrane repolarization during ventricular cardiac muscle cell action potential / membrane depolarization during action potential / potassium ion export across plasma membrane ...inward rectifier potassium channel complex / negative regulation of potassium ion export across plasma membrane / regulation of heart rate by hormone / Phase 3 - rapid repolarisation / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / negative regulation of potassium ion transmembrane transport / membrane repolarization during ventricular cardiac muscle cell action potential / membrane depolarization during action potential / potassium ion export across plasma membrane / membrane repolarization during cardiac muscle cell action potential / C3HC4-type RING finger domain binding / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / membrane repolarization / regulation of membrane repolarization / delayed rectifier potassium channel activity / positive regulation of potassium ion transmembrane transport / inward rectifier potassium channel activity / Voltage gated Potassium channels / potassium ion homeostasis / ventricular cardiac muscle cell action potential / regulation of potassium ion transmembrane transport / regulation of ventricular cardiac muscle cell membrane repolarization / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / voltage-gated potassium channel complex / cardiac muscle contraction / potassium ion transmembrane transport / regulation of membrane potential / cellular response to xenobiotic stimulus / scaffold protein binding / transcription cis-regulatory region binding / ubiquitin protein ligase binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, ERG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAC domain profile. / PAS domain / 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 ...Potassium channel, voltage-dependent, ERG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAC domain profile. / PAS domain / 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
Potassium voltage-gated channel subfamily H member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsAdaixo, R. / Morais-Cabral, J.H. / Harley, C.A.
CitationJournal: Plos One / Year: 2013
Title: Structural properties of PAS domains from the KCNH potassium channels
Authors: Adaixo, R. / Harley, C.A. / Castro-Rodrigues, A.F. / Morais-Cabral, J.H.
History
DepositionOct 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily H member 2


Theoretical massNumber of molelcules
Total (without water)15,4431
Polymers15,4431
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.750, 56.750, 134.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsThe biological unit is most likely a monomer. There is 1 biological unit in the asymmetric unit

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Components

#1: Protein Potassium voltage-gated channel subfamily H member 2 / Eag homolog / Ether-a-go-go-related gene potassium channel 1 / ERG-1 / Eag-related protein 1 / ...Eag homolog / Ether-a-go-go-related gene potassium channel 1 / ERG-1 / Eag-related protein 1 / Ether-a-go-go-related protein 1 / H-ERG / hERG-1 / hERG1 / Voltage-gated potassium channel subunit Kv11.1


Mass: 15442.942 Da / Num. of mol.: 1 / Fragment: PAS domain of KCNH channel, UNP residues 1-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERG, ERG1, HERG, KCNH2 / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q12809
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.03 Å3/Da / Density % sol: 39.4 % / Mosaicity: 0.59 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0M sodium/potassium tartrate, 0.1M Hepes, pH 7.0, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.96→49.138 Å / Num. all: 9923 / Num. obs: 9923 / % possible obs: 100 % / Observed criterion σ(F): 0.9 / Observed criterion σ(I): 0.9 / Redundancy: 16.7 % / Rsym value: 0.103 / Net I/σ(I): 21.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.96-2.0616.70.7470.7240.92303313800.1810.7470.7244.2100
2.06-2.1917.30.5270.5121.52325313410.1250.5270.5126100
2.19-2.3417.30.4010.3891.92153812470.0960.4010.3898100
2.34-2.5317.20.2690.2612.12020011740.0640.2690.26111.5100
2.53-2.77170.1960.193.91854110900.0470.1960.1916100
2.77-3.116.90.1180.1155.8169009990.0290.1180.11525.7100
3.1-3.5716.60.0740.0728.4149249010.0180.0740.07236.8100
3.57-4.3816.30.0510.04911.9125507700.0120.0510.04947.1100
4.38-6.1915.40.0490.04811.996706290.0120.0490.04856.3100
6.19-33.685130.0470.04511.151153920.0130.0470.04561.599.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BYW

1byw


Resolution: 1.96→33.169 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8485 / SU ML: 0.2 / σ(F): 0 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 476 4.82 %Random
Rwork0.2005 ---
all0.2023 9877 --
obs0.2023 9877 99.96 %-
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.424 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 97.29 Å2 / Biso mean: 39.6202 Å2 / Biso min: 16.95 Å2
Baniso -1Baniso -2Baniso -3
1-5.0643 Å20 Å2-0 Å2
2--5.0643 Å20 Å2
3----10.1286 Å2
Refinement stepCycle: LAST / Resolution: 1.96→33.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 0 0 40 902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004884
X-RAY DIFFRACTIONf_angle_d0.7971190
X-RAY DIFFRACTIONf_chiral_restr0.045132
X-RAY DIFFRACTIONf_plane_restr0.002157
X-RAY DIFFRACTIONf_dihedral_angle_d13.512335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.96-2.24130.25741760.236830043180
2.2413-2.82350.22521460.194230923238
2.8235-33.17390.23931540.194433053459
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.74730.81450.84726.2288-0.18155.17540.1925-0.139-0.616-0.2037-0.2077-0.43810.45040.0063-0.00280.169-0.0269-0.00730.17770.07490.336918.758913.303214.0372
25.48911.28710.30434.4948-1.14366.07080.2162-0.67490.30120.8318-0.4348-0.25910.1309-0.00580.19530.2936-0.0766-0.06650.2330.04940.232913.852214.194924.217
34.1052-0.83443.22594.079-0.70776.3138-0.4676-0.0668-0.22650.6739-0.3359-0.80350.83390.64840.76250.42430.02690.05250.1830.08980.375716.0945.923216.1915
46.2682.70382.37332.95211.4154.921-0.0325-0.5883-0.1350.0148-0.10390.27160.5734-1.36610.03250.3893-0.2465-0.07780.50320.00180.21293.59566.374717.5106
55.9262-1.31890.60126.71481.61182.19270.16650.2571-0.6356-0.0027-0.7490.5050.3784-1.80990.54090.5654-0.2483-0.05850.6445-0.07020.30821.33575.83936.6059
68.4680.88430.07376.1938-2.33643.18490.65241.5195-0.7842-1.73520.4756-0.32910.7089-0.337-0.55610.5355-0.1572-0.03670.22940.01190.345511.48287.50683.7604
75.7848-2.1959-4.3874.3623.46894.2677-0.24561.0709-0.2695-1.54730.2552-0.9402-0.1515-0.392-0.06810.50060.1328-0.04750.45670.07140.38910.120615.01211.8326
81.95040.8545-0.86761.8799-0.32753.55240.2212-0.8950.3525-0.176-0.81670.3480.1159-0.72380.27080.0652-0.2401-0.0090.6383-0.07350.24342.907313.284517.2253
92.39242.5296-0.87634.4808-2.55097.6910.14890.514-0.7574-1.13560.2364-1.02370.34430.5871-0.03410.4036-0.03910.1750.32920.00150.441822.842815.35922.8755
104.1448-3.1040.03063.85742.13973.15370.14360.46810.6854-0.1331-0.3674-0.1064-0.9729-1.85240.04640.30390.057-0.0530.50510.06380.28225.342819.138414.4559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 26:44)A26 - 44
2X-RAY DIFFRACTION2(chain A and resid 45:60)A45 - 60
3X-RAY DIFFRACTION3(chain A and resid 61:65)A61 - 65
4X-RAY DIFFRACTION4(chain A and resid 66:74)A66 - 74
5X-RAY DIFFRACTION5(chain A and resid 75:81)A75 - 81
6X-RAY DIFFRACTION6(chain A and resid 82:88)A82 - 88
7X-RAY DIFFRACTION7(chain A and resid 89:93)A89 - 93
8X-RAY DIFFRACTION8(chain A and resid 94:112)A94 - 112
9X-RAY DIFFRACTION9(chain A and resid 113:126)A113 - 126
10X-RAY DIFFRACTION10(chain A and resid 127:133)A127 - 133

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