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- PDB-6syg: Crystal structure of the Cyclic Nucleotide-Binding Homology Domai... -

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Basic information

Entry
Database: PDB / ID: 6syg
TitleCrystal structure of the Cyclic Nucleotide-Binding Homology Domain of the human KCNH2 channel
ComponentsPotassium voltage-gated channel subfamily H member 2
KeywordsTRANSPORT PROTEIN / Intracellular domain / CNBHD / hERG
Function / homology
Function and homology information


Phase 3 - rapid repolarisation / inward rectifier potassium channel complex / negative regulation of potassium ion export across plasma membrane / regulation of heart rate by hormone / cellular response to xenobiotic stimulus => GO:0071466 / Phase 3 - rapid repolarisation / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / Voltage gated Potassium channels / membrane repolarization during ventricular cardiac muscle cell action potential ...Phase 3 - rapid repolarisation / inward rectifier potassium channel complex / negative regulation of potassium ion export across plasma membrane / regulation of heart rate by hormone / cellular response to xenobiotic stimulus => GO:0071466 / Phase 3 - rapid repolarisation / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / Voltage gated Potassium channels / membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of potassium ion transmembrane transport / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / C3HC4-type RING finger domain binding / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of membrane repolarization / membrane repolarization / positive regulation of potassium ion transmembrane transport / Voltage gated Potassium channels / inward rectifier potassium channel activity / potassium ion homeostasis / ventricular cardiac muscle cell action potential / regulation of potassium ion transmembrane transport / regulation of ventricular cardiac muscle cell membrane repolarization / delayed rectifier potassium channel activity / membrane depolarization during action potential / spinal cord development / voltage-gated potassium channel activity / potassium channel activity / regulation of heart rate by cardiac conduction / plasma membrane => GO:0005886 / potassium ion import across plasma membrane / cardiac muscle contraction / potassium ion transmembrane transport / voltage-gated potassium channel complex / regulation of membrane potential / potassium ion transport / brain development / cellular response to xenobiotic stimulus / nuclear envelope / monoatomic ion channel activity / scaffold protein binding / transcription cis-regulatory region binding / ubiquitin protein ligase binding / protein-containing complex binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm
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) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...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) / 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 / Voltage-dependent channel domain superfamily / 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 2 / Potassium voltage-gated channel subfamily H member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBen-Bassat, A. / Giladi, M. / Haitin, Y.
Funding support Israel, 4items
OrganizationGrant numberCountry
Israel Science Foundation1721/16 Israel
Israel Science Foundation1775/12 Israel
Other privateICRF 01214 Israel
German-Israeli Foundation for Research and DevelopmentI-2425-418.13/2016 Israel
CitationJournal: J.Gen.Physiol. / Year: 2020
Title: Structure of KCNH2 cyclic nucleotide-binding homology domain reveals a functionally vital salt-bridge.
Authors: Ben-Bassat, A. / Giladi, M. / Haitin, Y.
History
DepositionSep 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 18, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy / Structure summary
Category: atom_site / entity_name_com ...atom_site / entity_name_com / entity_src_gen / pdbx_nonpoly_scheme / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 2.1Apr 15, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 3.0Apr 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_symm_contact / refine / refine_hist / refine_ls_restr / refine_ls_shell / software
Item: _entity.pdbx_number_of_molecules / _pdbx_distant_solvent_atoms.auth_seq_id ..._entity.pdbx_number_of_molecules / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_prop.value / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number
Description: Model completeness / Details: OXT added to the C-terminal residue. / Provider: author / Type: Coordinate replacement
Revision 3.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,0661
Polymers15,0661
Non-polymers00
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.493, 90.649, 61.111
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-910-

HOH

21A-923-

HOH

31A-956-

HOH

41A-1066-

HOH

51A-1124-

HOH

61A-1187-

HOH

71A-1188-

HOH

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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 / hERG1 / Voltage-gated potassium ...Eag homolog / Ether-a-go-go-related gene potassium channel 1 / hERG1 / Voltage-gated potassium channel subunit Kv11.1


Mass: 15066.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNH2, ERG, ERG1, HERG / Production host: Escherichia coli (E. coli) / References: UniProt: Q12809, UniProt: O08962*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 3350, 2% v/v Tacsimate, 0.1M Bis-Tris, pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.5→48.58 Å / Num. obs: 25875 / % possible obs: 99.7 % / Redundancy: 11.5 % / Biso Wilson estimate: 14.67 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.114 / Net I/σ(I): 13.91
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 4087 / Rrim(I) all: 0.811

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4llo

4llo


Resolution: 1.5→48.55 Å / SU ML: 0.1555 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 19.6688
RfactorNum. reflection% reflection
Rfree0.184 1297 5.01 %
Rwork0.1702 24578 -
obs0.1706 25875 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.95 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 0 297 1345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821098
X-RAY DIFFRACTIONf_angle_d1.05831495
X-RAY DIFFRACTIONf_chiral_restr0.0673168
X-RAY DIFFRACTIONf_plane_restr0.0071194
X-RAY DIFFRACTIONf_dihedral_angle_d10.7606894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.560.26661430.23572642X-RAY DIFFRACTION98.55
1.56-1.630.25661300.20682722X-RAY DIFFRACTION99.96
1.63-1.720.22741360.19032707X-RAY DIFFRACTION99.96
1.72-1.820.19481460.18262694X-RAY DIFFRACTION99.86
1.82-1.970.22321550.18282705X-RAY DIFFRACTION99.97
1.97-2.160.17141480.15612720X-RAY DIFFRACTION99.97
2.16-2.480.17941510.16692742X-RAY DIFFRACTION99.9
2.48-3.120.16481380.16652767X-RAY DIFFRACTION99.86
3.12-48.550.16521500.15622879X-RAY DIFFRACTION99.84
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)
10.304383527183-0.218186393792-0.1103166197920.41302967414-0.05970545617950.432920666021-0.0394856019538-0.0107874865761-0.220520689857-0.1973974004630.1393279331720.1421290696990.120476625323-0.0737358834440.08392766529860.18536310741-0.0173065624688-0.0112109962170.1067825082570.02294258581730.106466583869-12.2956394634-22.5675241326.09194719724
20.370485124369-0.102586284103-0.3645810680030.02575765721130.09417790983010.372224813501-0.0183836291396-0.0984614062471-0.06744504531040.05702648008680.03845809022530.136786069416-0.0844998508428-0.320697477536-0.001803632473370.141400347090.0101561321038-0.009251627108130.140808041197-0.001473583732190.119214136003-15.417203843-13.95285028427.84474233148
30.1467386523060.3343596947960.02772459522070.7576525039220.04372609749180.2705513126650.0101663365445-0.09510170826550.404841431949-0.040121016002-0.01013462819280.29840665868-0.0513621870417-0.05394359339910.02677183369520.0860311748802-0.00848715770784-0.004790322882360.112205662609-0.0245662866570.112584740666-17.7587913698-6.45421717611-10.9229756546
40.568706496052-0.234452718670.5000222603930.674093802166-0.05350056286190.473189403912-0.0263693190766-0.103675338496-0.09534317693960.04440801889170.125014476285-0.121968245517-0.191014978507-0.06809932895820.05652384885050.0957214417805-0.0165203367219-0.003454194490010.111093007948-0.000924110566020.0782974591514-16.3881987182-15.541191138-9.94102279624
50.363916218223-0.1195897904220.1180150610660.4980776070280.3577236265170.378747354732-0.0319405380283-0.0270759789834-0.0297677043543-0.08030796503710.0335046537432-0.121907879227-0.0921090283375-0.008675468077730.001711904497230.131357000955-0.0122567993973-0.002013615249010.11173751477-0.001943453740740.117637294417-13.0626807805-15.6211694217-12.9293720842
60.299661560716-0.00948525033648-0.09485008805270.544566025997-0.09511653762040.0455728196578-0.0153970013679-0.159980448248-0.0353339380483-0.00982613173365-0.0245872331279-0.122230631473-0.0682186563395-0.05243031420240.004457193081560.0808563880134-0.0129545780311-0.01106125042960.1115440094380.005406009185060.0982120678778-11.3483303838-8.63799676134-10.6830045405
71.90672948150.1371423472220.4557210002360.9168239162680.3431244905791.12159655638-0.0168031395214-0.2136400009210.1243383525280.1202931091660.0136033145757-0.0756300831291-0.15918301348-0.1911230026380.153916914360.1038894204170.00397673748233-0.02960420356910.0969525020660.007569805277770.114265879893-10.7974634214-10.00304611752.77516969868
80.2074701143370.0706582637804-0.008496094838130.126154211068-0.006958759073930.0926171308003-0.0179083059772-0.126707719599-0.05101647501620.0222418627056-0.118231660626-0.2832521922790.420313058040.363928324795-0.008639925632190.1955117711130.0395461858737-0.005477792609050.1823541345590.01652419890580.162860618863-0.304872376377-17.39764213584.7026791734
91.04006761541-0.2012812473250.0003952310868830.08410501674020.1666890896220.607221467353-0.006118578847460.309515722016-0.004547091947260.000564429925310.0115249967959-0.198649368335-0.03152742351760.1558168320620.02712678959930.0946197010023-0.00405126118545-0.01658020354680.103592424285-0.009235192615730.120304686913-5.92239958366-13.4739741514-11.3656312711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 730 through 747 )
2X-RAY DIFFRACTION2chain 'A' and (resid 748 through 763 )
3X-RAY DIFFRACTION3chain 'A' and (resid 764 through 777 )
4X-RAY DIFFRACTION4chain 'A' and (resid 778 through 791 )
5X-RAY DIFFRACTION5chain 'A' and (resid 792 through 809 )
6X-RAY DIFFRACTION6chain 'A' and (resid 810 through 827 )
7X-RAY DIFFRACTION7chain 'A' and (resid 828 through 844 )
8X-RAY DIFFRACTION8chain 'A' and (resid 845 through 855 )
9X-RAY DIFFRACTION9chain 'A' and (resid 856 through 864 )

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