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- PDB-6y7q: Crystal Structure of the N-terminal PAS domain from the hERG3 Pot... -

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Basic information

Entry
Database: PDB / ID: 6y7q
TitleCrystal Structure of the N-terminal PAS domain from the hERG3 Potassium Channel
ComponentsPotassium voltage-gated channel subfamily H member 7
KeywordsMEMBRANE PROTEIN / PAS / Potassium Channel / Heme Binding / Rossmann Fold
Function / homology
Function and homology information


Voltage gated Potassium channels / regulation of monoatomic ion transmembrane transport / voltage-gated potassium channel activity / plasma membrane => GO:0005886 / potassium ion transmembrane transport / regulation of membrane potential / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, ERG / Potassium channel, voltage-dependent, EAG/ELK/ERG / 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 / Voltage-dependent channel domain superfamily / PAS domain ...Potassium channel, voltage-dependent, ERG / Potassium channel, voltage-dependent, EAG/ELK/ERG / 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 / Voltage-dependent channel domain superfamily / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily H member 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsCresser-Brown, J. / Raven, E. / Moody, P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/K000128/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M018598/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Discovery of a heme-binding domain in a neuronal voltage-gated potassium channel.
Authors: Burton, M.J. / Cresser-Brown, J. / Thomas, M. / Portolano, N. / Basran, J. / Freeman, S.L. / Kwon, H. / Bottrill, A.R. / Llansola-Portoles, M.J. / Pascal, A.A. / Jukes-Jones, R. / Chernova, ...Authors: Burton, M.J. / Cresser-Brown, J. / Thomas, M. / Portolano, N. / Basran, J. / Freeman, S.L. / Kwon, H. / Bottrill, A.R. / Llansola-Portoles, M.J. / Pascal, A.A. / Jukes-Jones, R. / Chernova, T. / Schmid, R. / Davies, N.W. / Storey, N.M. / Dorlet, P. / Moody, P.C.E. / Mitcheson, J.S. / Raven, E.L.
History
DepositionMar 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Potassium voltage-gated channel subfamily H member 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6094
Polymers15,3931
Non-polymers2163
Water1,11762
1
AAA: Potassium voltage-gated channel subfamily H member 7
hetero molecules

AAA: Potassium voltage-gated channel subfamily H member 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2188
Polymers30,7852
Non-polymers4326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2720 Å2
ΔGint-10 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.784, 32.784, 200.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Potassium voltage-gated channel subfamily H member 7 / Ether-a-go-go-related gene potassium channel 3 / hERG-3 / Voltage-gated potassium channel subunit Kv11.3


Mass: 15392.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNH7, ERG3 / Plasmid: pLEICS-93 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NS40
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.75 Å3/Da / Density % sol: 29.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: hERG3 PAS domain (15 mg/ml, in 50 mM NaCl, 1 mM TCEP in a 1:1 ratio with reservoir solution (0.1 M NaCl, 0.1 M HEPES pH=7.5, 1.6 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.39→66.9 Å / Num. obs: 23496 / % possible obs: 100 % / Redundancy: 11.9656537283 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.39-1.4317090.7661
6.22-66.93710.9991

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HQA

4hqa


Resolution: 1.39→50.221 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 7.176 / SU ML: 0.107 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2352 1208 5.167 %
Rwork0.1843 --
all0.187 --
obs-22170 99.983 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.173 Å2
Baniso -1Baniso -2Baniso -3
1--1.748 Å2-0 Å2-0 Å2
2---1.748 Å20 Å2
3---3.496 Å2
Refinement stepCycle: LAST / Resolution: 1.39→50.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 14 62 1013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.013975
X-RAY DIFFRACTIONr_bond_other_d0.010.017893
X-RAY DIFFRACTIONr_angle_refined_deg2.2341.6531310
X-RAY DIFFRACTIONr_angle_other_deg1.6461.5752079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1355118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00323.20853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.96115172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.681155
X-RAY DIFFRACTIONr_chiral_restr0.1240.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021088
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02204
X-RAY DIFFRACTIONr_nbd_refined0.2360.2203
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2570.2885
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2476
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.2465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.250
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.6650.217
X-RAY DIFFRACTIONr_nbd_other0.6180.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3010.210
X-RAY DIFFRACTIONr_mcbond_it4.5982.961472
X-RAY DIFFRACTIONr_mcbond_other4.5692.956471
X-RAY DIFFRACTIONr_mcangle_it5.4354.457590
X-RAY DIFFRACTIONr_mcangle_other5.4324.461591
X-RAY DIFFRACTIONr_scbond_it7.9913.659503
X-RAY DIFFRACTIONr_scbond_other7.9853.661504
X-RAY DIFFRACTIONr_scangle_it9.4615.237720
X-RAY DIFFRACTIONr_scangle_other9.4545.238721
X-RAY DIFFRACTIONr_lrange_it9.0538.2531092
X-RAY DIFFRACTIONr_lrange_other938.1541089
X-RAY DIFFRACTIONr_rigid_bond_restr18.19531868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.426-1.4650.339900.2751525X-RAY DIFFRACTION99.9381
1.465-1.5080.328770.271507X-RAY DIFFRACTION100
1.508-1.5540.253830.2441493X-RAY DIFFRACTION100
1.554-1.6050.297910.2081390X-RAY DIFFRACTION100
1.605-1.6610.343760.2311402X-RAY DIFFRACTION100
1.661-1.7240.322550.2161372X-RAY DIFFRACTION100
1.724-1.7940.281610.1851287X-RAY DIFFRACTION100
1.794-1.8740.235730.2021232X-RAY DIFFRACTION100
1.874-1.9650.231640.191199X-RAY DIFFRACTION100
1.965-2.0710.239550.1771156X-RAY DIFFRACTION99.9175
2.071-2.1970.297510.1731105X-RAY DIFFRACTION100
2.197-2.3480.236520.1621029X-RAY DIFFRACTION100
2.348-2.5360.216510.146963X-RAY DIFFRACTION100
2.536-2.7780.248640.157866X-RAY DIFFRACTION100
2.778-3.1050.212470.179819X-RAY DIFFRACTION100
3.105-3.5840.194430.163739X-RAY DIFFRACTION100
3.584-4.3870.187310.158630X-RAY DIFFRACTION100
4.387-6.1910.232350.179516X-RAY DIFFRACTION100
6.191-50.2210.241160.269332X-RAY DIFFRACTION100

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