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

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Basic information

Entry
Database: PDB / ID: 4xdj
TitleCrystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in an alternate conformation (FORM 2)
ComponentsPOTASSIUM CHANNEL SUBFAMILY K MEMBER 10
KeywordsTRANSPORT PROTEIN / OUTWARD RECTIFICATION / MEMBRANE PROTEIN / K2P / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


TWIK related potassium channel (TREK) / cellular response to arachidonate / mechanosensitive potassium channel activity / Phase 4 - resting membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / monoatomic ion channel complex / potassium channel activity / potassium ion transmembrane transport / signal transduction / 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
: / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / TRIDECANE / Potassium channel subfamily K member 10
Similarity search - Component
Biological specieshomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsPike, A.C.W. / Dong, Y.Y. / Mackenzie, A. / Mukhopadhyay, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Burgess-Brown, N.A. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust092809/Z/10/Z United Kingdom
CitationJournal: Science / Year: 2015
Title: K2P channel gating mechanisms revealed by structures of TREK-2 and a complex with Prozac.
Authors: Dong, Y.Y. / Pike, A.C. / Mackenzie, A. / McClenaghan, C. / Aryal, P. / Dong, L. / Quigley, A. / Grieben, M. / Goubin, S. / Mukhopadhyay, S. / Ruda, G.F. / Clausen, M.V. / Cao, L. / Brennan, ...Authors: Dong, Y.Y. / Pike, A.C. / Mackenzie, A. / McClenaghan, C. / Aryal, P. / Dong, L. / Quigley, A. / Grieben, M. / Goubin, S. / Mukhopadhyay, S. / Ruda, G.F. / Clausen, M.V. / Cao, L. / Brennan, P.E. / Burgess-Brown, N.A. / Sansom, M.S. / Tucker, S.J. / Carpenter, E.P.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 10
B: POTASSIUM CHANNEL SUBFAMILY K MEMBER 10
C: POTASSIUM CHANNEL SUBFAMILY K MEMBER 10
D: POTASSIUM CHANNEL SUBFAMILY K MEMBER 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,37318
Polymers124,2404
Non-polymers4,13314
Water00
1
A: POTASSIUM CHANNEL SUBFAMILY K MEMBER 10
B: POTASSIUM CHANNEL SUBFAMILY K MEMBER 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,76711
Polymers62,1202
Non-polymers3,6479
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12300 Å2
ΔGint-119 kcal/mol
Surface area23970 Å2
MethodPISA
2
C: POTASSIUM CHANNEL SUBFAMILY K MEMBER 10
D: POTASSIUM CHANNEL SUBFAMILY K MEMBER 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6067
Polymers62,1202
Non-polymers4865
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-92 kcal/mol
Surface area22080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.745, 113.871, 111.782
Angle α, β, γ (deg.)90.00, 90.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
POTASSIUM CHANNEL SUBFAMILY K MEMBER 10


Mass: 31060.111 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 67-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) homo sapiens (human) / Plasmid: PFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P57789
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#4: Chemical
ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H28
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M KCl, 0.1M sodium cacodylate pH6.5, 22% (w/v) PEG1500 + 3% (v/v) Methanol

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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: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.8→38.37 Å / Num. obs: 18910 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 129.62 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 1.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BW5

4bw5


Resolution: 3.8→37.26 Å / Cor.coef. Fo:Fc: 0.8426 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.614
RfactorNum. reflection% reflectionSelection details
Rfree0.2769 978 5.18 %RANDOM
Rwork0.2629 ---
obs0.2637 18895 99.03 %-
Displacement parametersBiso mean: 164.38 Å2
Baniso -1Baniso -2Baniso -3
1--29.4201 Å20 Å2-2.2118 Å2
2--21.4978 Å20 Å2
3---7.9223 Å2
Refine analyzeLuzzati coordinate error obs: 1.129 Å
Refinement stepCycle: 1 / Resolution: 3.8→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6959 0 99 0 7058
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097222HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.99860HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3026SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1095HARMONIC5
X-RAY DIFFRACTIONt_it7222HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.81
X-RAY DIFFRACTIONt_other_torsion2.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1009SEMIHARMONIC5
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_contact8829SEMIHARMONIC4
LS refinement shellResolution: 3.8→4.03 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2972 136 4.47 %
Rwork0.244 2907 -
all0.2463 3043 -
obs--99.03 %
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)
11.8351-0.2343-0.20294.33261.46734.4210.15470.15450.1858-0.37440.101-0.58430.28180.3168-0.2558-0.46670.04710.0955-0.3061-0.0519-0.1514Chain A21.308623.434254.3499
21.8628-0.3903-0.8714.69081.67064.51830.19450.14880.0502-0.3109-0.23840.3590.3395-0.81890.0439-0.5443-0.0597-0.076-0.2293-0.0433-0.2708Chain B9.43121.418357.4827
31.7407-0.63160.219912.7559-6.82128.51940.0516-0.1249-0.191.18470.07471.3392-0.3137-0.0218-0.1263-0.5076-0.00720.3169-0.53620.3294-0.1882Chain C52.987320.30121.8675
41.58940.1178-1.177618.3179-8.73058.4033-0.07140.2017-0.5703-0.29070.17431.2651.2284-0.0835-0.1029-0.47250.02840.1274-0.52910.1983-0.3183Chain D55.287110.5158-4.4855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{D|73 - 332}
2X-RAY DIFFRACTION2{B|73 - 332}
3X-RAY DIFFRACTION3{C|74 - 603}
4X-RAY DIFFRACTION4{D|73 - 332}

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