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- PDB-4hp9: Crystal structure of the N-terminal truncated PAS domain from the... -

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Basic information

Entry
Database: PDB / ID: 4hp9
TitleCrystal structure of the N-terminal truncated PAS domain from the hERG potassium channel
ComponentsPotassium voltage-gated channel subfamily H member 2
KeywordsTRANSPORT PROTEIN / Potassium channel domain
Function / homology
Function and homology information


regulation of heart rate by hormone / inward rectifier potassium channel complex / Phase 3 - rapid repolarisation / membrane repolarization during action potential / negative regulation of potassium ion export across plasma membrane / negative regulation of potassium ion transmembrane transport / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization ...regulation of heart rate by hormone / inward rectifier potassium channel complex / Phase 3 - rapid repolarisation / membrane repolarization during action potential / negative regulation of potassium ion export across plasma membrane / negative regulation of potassium ion transmembrane transport / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of membrane repolarization / membrane repolarization / membrane depolarization during action potential / delayed rectifier potassium channel activity / ventricular cardiac muscle cell action potential / inward rectifier potassium channel activity / potassium ion homeostasis / Voltage gated Potassium channels / regulation of ventricular cardiac muscle cell membrane repolarization / positive regulation of potassium ion transmembrane transport / regulation of potassium ion transmembrane transport / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / cardiac muscle contraction / voltage-gated potassium channel complex / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / cellular response to xenobiotic stimulus / scaffold protein binding / transcription cis-regulatory region binding / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / 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 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, ERG / : / 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 inwardly rectifying potassium channel KCNH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 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 23, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,4361
Polymers14,4361
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.528, 89.528, 89.528
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number208
Space group name H-MP4232

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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: 14435.706 Da / Num. of mol.: 1 / Fragment: PAS domain of KCNH channel, UNP residues 10-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERG, ERG1, HERG, KCNH2 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q12809
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.07 Å3/Da / Density % sol: 40.61 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 30% PEG-MME2000, 0.1M potasiumm thiocyanate, 1.0% benzamidine-HCl, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0015 Å
DetectorType: MARCCD / Detector: CCD / Date: Oct 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 2.12→89.528 Å / Num. all: 7429 / Num. obs: 7429 / % possible obs: 99.5 % / Observed criterion σ(F): 1.45 / Observed criterion σ(I): 1.1 / Redundancy: 9.9 % / Rsym value: 0.089 / Net I/σ(I): 21.7
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
2.12-2.237.80.7830.6911.1797910200.270.7830.6912.997.1
2.23-2.3710.50.4550.4121.9103409880.1390.4550.4125.799.7
2.37-2.5310.50.2970.272.9100479560.090.2970.278.6100
2.53-2.7410.50.2310.213.791348720.0710.2310.2110.7100
2.74-310.40.1480.1355.885818240.0450.1480.13516.3100
3-3.3510.30.080.07310.676237420.0250.080.07328.4100
3.35-3.8710.20.0530.04815.468986750.0170.0530.04839.4100
3.87-4.749.80.0390.03619.856895790.0120.0390.03653.3100
4.74-6.79.50.040.0362044864710.0130.040.03651.6100
6.7-89.52880.0230.02129.924173020.0080.0230.02162100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BYW

1byw


Resolution: 2.12→44.764 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.798 / SU ML: 0.25 / σ(F): 1.46 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.238 642 4.9 %random
Rwork0.1937 ---
obs0.1959 7403 99.18 %-
all-13112 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.305 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso max: 82.52 Å2 / Biso mean: 27.7094 Å2 / Biso min: 10.61 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.12→44.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 0 89 1003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008920
X-RAY DIFFRACTIONf_angle_d1.0331241
X-RAY DIFFRACTIONf_chiral_restr0.064141
X-RAY DIFFRACTIONf_plane_restr0.003164
X-RAY DIFFRACTIONf_dihedral_angle_d14.345334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.12-2.28260.38591290.31442425255496
2.2826-2.51230.26131250.216125022627100
2.5123-2.87580.26451250.197825162641100
2.8758-3.6230.22561350.184825102645100
3.623-44.7740.18311280.159325172645100

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