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- PDB-4twk: Crystal structure of human two pore domain potassium ion channel ... -

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Basic information

Entry
Database: PDB / ID: 4twk
TitleCrystal structure of human two pore domain potassium ion channel TREK1 (K2P2.1)
ComponentsPotassium channel subfamily K member 2
KeywordsTRANSPORT PROTEIN / Ion channel / Membrane protein / K2P
Function / homology
Function and homology information


TWIK related potassium channel (TREK) / : / Phase 4 - resting membrane potential / positive regulation of cellular response to hypoxia / cardiac ventricle development / stabilization of membrane potential / potassium ion leak channel activity / negative regulation of cardiac muscle cell proliferation / astrocyte projection / potassium channel inhibitor activity ...TWIK related potassium channel (TREK) / : / Phase 4 - resting membrane potential / positive regulation of cellular response to hypoxia / cardiac ventricle development / stabilization of membrane potential / potassium ion leak channel activity / negative regulation of cardiac muscle cell proliferation / astrocyte projection / potassium channel inhibitor activity / outward rectifier potassium channel activity / negative regulation of DNA biosynthetic process / cochlea development / plasma membrane => GO:0005886 / calyx of Held / response to axon injury / voltage-gated potassium channel complex / response to mechanical stimulus / potassium ion transmembrane transport / memory / cellular response to hypoxia / G protein-coupled receptor signaling pathway / apical plasma membrane / neuronal cell body / endoplasmic reticulum membrane / cell surface / endoplasmic reticulum / nucleus / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TREK / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Octyl Glucose Neopentyl Glycol / : / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPike, A.C.W. / Dong, Y.Y. / Tessitore, A. / Goubin, S. / Strain-Damerell, C. / Mukhopadhyay, S. / Kupinska, K. / Wang, D. / Chalk, R. / Berridge, G. ...Pike, A.C.W. / Dong, Y.Y. / Tessitore, A. / Goubin, S. / Strain-Damerell, C. / Mukhopadhyay, S. / Kupinska, K. / Wang, D. / Chalk, R. / Berridge, G. / Grieben, M. / Shrestha, L. / Ang, J.H. / Mackenzie, A. / Quigley, A. / Bushell, S.R. / Shintre, C.A. / Faust, B. / Chu, A. / Dong, L. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Burgess-Brown, N.A. / Carpenter, E.P.
CitationJournal: To Be Published
Title: Crystal structure of human two pore domain potassium ion channel TREK1 (K2P2.1)
Authors: Pike, A.C.W. / Dong, Y.Y. / Tessitore, A. / Goubin, S. / Strain-Damerell, C. / Mukhopadhyay, S. / Kupinska, K. / Wang, D. / Chalk, R. / Berridge, G. / Grieben, M. / Shrestha, L. / Ang, J.H. ...Authors: Pike, A.C.W. / Dong, Y.Y. / Tessitore, A. / Goubin, S. / Strain-Damerell, C. / Mukhopadhyay, S. / Kupinska, K. / Wang, D. / Chalk, R. / Berridge, G. / Grieben, M. / Shrestha, L. / Ang, J.H. / Mackenzie, A. / Quigley, A. / Bushell, S.R. / Shintre, C.A. / Faust, B. / Chu, A. / Dong, L. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Burgess-Brown, N.A. / Carpenter, E.P.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 channel subfamily K member 2
B: Potassium channel subfamily K member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,66512
Polymers62,4592
Non-polymers3,20610
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12740 Å2
ΔGint-109 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.470, 105.975, 128.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Potassium channel subfamily K member 2 / Outward rectifying potassium channel protein TREK-1 / TREK-1 K(+) channel subunit / Two pore domain ...Outward rectifying potassium channel protein TREK-1 / TREK-1 K(+) channel subunit / Two pore domain potassium channel TREK-1 / Two pore potassium channel TPKC1


Mass: 31229.432 Da / Num. of mol.: 2 / Fragment: UNP residues 26-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK2, TREK, TREK1 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O95069
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 36 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-37X / Octyl Glucose Neopentyl Glycol


Mass: 568.695 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H52O12
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.68 % / Description: Rods
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.25M magnesium formate, 0.1M Sodium Cacodylate pH 6.5, 17% PEG3000, 5% PEG400
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.6→39.65 Å / Num. all: 31773 / Num. obs: 31773 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 74.16 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.5
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.836 / Mean I/σ(I) obs: 1.1 / % possible all: 93.1

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BW5

4bw5


Resolution: 2.6→33.94 Å / Cor.coef. Fo:Fc: 0.8906 / Cor.coef. Fo:Fc free: 0.8909 / SU R Cruickshank DPI: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.288 / SU Rfree Blow DPI: 0.23 / SU Rfree Cruickshank DPI: 0.237
Details: DIFFRACTION DATA WERE SEVERELY ANISOTROPIC ALL DATA TO 2.6A WAS USED IN REFINEMENT WITHOUT TRUNCATION. NOMINAL RESOLUTION IS 2.8A BASED ON MN (I)/SD(I)>2 CRITERIA
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1607 5.07 %RANDOM
Rwork0.2308 ---
obs0.2322 31710 99.4 %-
Displacement parametersBiso mean: 113.28 Å2
Baniso -1Baniso -2Baniso -3
1--8.0728 Å20 Å20 Å2
2---20.667 Å20 Å2
3---28.7397 Å2
Refine analyzeLuzzati coordinate error obs: 0.522 Å
Refinement stepCycle: 1 / Resolution: 2.6→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 168 27 3941
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094005HARMONIC2
X-RAY DIFFRACTIONt_angle_deg15468HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1769SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes571HARMONIC5
X-RAY DIFFRACTIONt_it4005HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.22
X-RAY DIFFRACTIONt_other_torsion2.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion592SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4902SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.1829 151 5.59 %
Rwork0.1901 2549 -
all0.1897 2700 -
obs--99.4 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
11.9839-0.8042-1.32812.38190.83967.3875-0.20220.1107-0.09810.05850.10140.02420.0098-0.7110.1008-0.39020.0587-0.0463-0.2826-0.0544-0.3534Chain A14.2202-1.5973-24.9434
22.3033-0.7249-0.97811.8665-0.00636.9659-0.1476-0.41460.05970.25630.2551-0.4413-0.50920.7804-0.1074-0.39440.0612-0.1044-0.3104-0.1166-0.3706Chain B24.6672.8693-17.0848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|38 - 408}
2X-RAY DIFFRACTION2{B|42 - 750} Includes NAG glycosylation on B95

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