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- PDB-4bw5: Crystal structure of human two pore domain potassium ion channel ... -

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Basic information

Entry
Database: PDB / ID: 4bw5
TitleCrystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1)
ComponentsPOTASSIUM CHANNEL SUBFAMILY K MEMBER 10
KeywordsTRANSPORT PROTEIN / OUTWARD RECTIFICATION / MEMBRANE PROTEIN / K2P
Function / homology
Function and homology information


TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / monoatomic ion channel complex / potassium channel activity / potassium ion transmembrane transport / memory / 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 / Potassium channel subfamily K member 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPike, A.C.W. / Dong, Y.Y. / Dong, L. / Quigley, A. / Shrestha, L. / Mukhopadhyay, S. / Strain-Damerell, C. / Goubin, S. / Grieben, M. / Shintre, C.A. ...Pike, A.C.W. / Dong, Y.Y. / Dong, L. / Quigley, A. / Shrestha, L. / Mukhopadhyay, S. / Strain-Damerell, C. / Goubin, S. / Grieben, M. / Shintre, C.A. / Mackenzie, A. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Burgess-Brown, N. / Carpenter, E.P.
CitationJournal: Science / Year: 2015
Title: K2P Channel Gating Mechanisms Revealed by Structures of Trek-2 and a Complex with Prozac
Authors: Pike, A.C.W. / 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. / ...Authors: Pike, A.C.W. / 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.P. / Tucker, S.J. / Carpenter, E.P.
History
DepositionJun 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)126,35816
Polymers124,2404
Non-polymers2,11812
Water0
1
A: POTASSIUM CHANNEL SUBFAMILY K MEMBER 10
B: POTASSIUM CHANNEL SUBFAMILY K MEMBER 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,08210
Polymers62,1202
Non-polymers1,9628
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11330 Å2
ΔGint-124.4 kcal/mol
Surface area23880 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)62,2776
Polymers62,1202
Non-polymers1564
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-111.1 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.830, 96.960, 103.700
Angle α, β, γ (deg.)90.00, 92.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.714, -0.498, -0.491), (-0.466, -0.185, 0.865), (-0.522, 0.847, -0.1)57.38622, 55.8852, -21.20921
2given(0.117, -0.622, 0.775), (-0.717, -0.592, -0.367), (0.687, -0.513, -0.515)41.72997, 131.23695, 58.17944
3given(-0.177, 0.715, -0.676), (0.984, 0.142, -0.107), (0.02, -0.684, -0.729)-3.12131, 65.07817, 79.45943

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Components

#1: Protein
POTASSIUM CHANNEL SUBFAMILY K MEMBER 10 / OUTWARD RECTIFYING POTASSIUM CHANNEL PROTEIN TREK-2 / TREK-2 K(+) CHANNEL SUBUNIT


Mass: 31060.111 Da / Num. of mol.: 4 / Fragment: ISOFORM C, RESIDUES 67-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-CT10HF-LIC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P57789
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM

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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: 3.55 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growTemperature: 277 K / pH: 8
Details: 0.001M CADMIUM CHLORIDE, 0.2M POTASSIUM CHLORIDE,31%(V/V) PEG400,0.1M HEPES PH 8.0, 2% (W/V) BENZAMIDINE, TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.2→39.57 Å / Num. obs: 28707 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 143.85 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.7
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.1 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3UM7, 3UKM

3um7

3ukm


Resolution: 3.2→39.57 Å / Cor.coef. Fo:Fc: 0.9067 / Cor.coef. Fo:Fc free: 0.9112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.673 / SU Rfree Blow DPI: 0.39
Details: DIFFRACTION DATA WERE SEVERELY ANISOTROPI ALL DATA TO 3.2A WAS USED IN REFINEMENT WITHOUT TRUNCATION. NOMINAL RESOLUTION IS 3.4A BASED ON MN (I)/SD(I)>2 CRITERIA
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1458 5.08 %RANDOM
Rwork0.2369 ---
obs0.2377 28689 99.29 %-
Displacement parametersBiso mean: 155.24 Å2
Baniso -1Baniso -2Baniso -3
1--9.2052 Å20 Å2-24.0457 Å2
2--4.3948 Å20 Å2
3---4.8105 Å2
Refine analyzeLuzzati coordinate error obs: 0.959 Å
Refinement stepCycle: LAST / Resolution: 3.2→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7203 0 32 0 7235
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097407HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9310140HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3096SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1124HARMONIC5
X-RAY DIFFRACTIONt_it7407HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.99
X-RAY DIFFRACTIONt_other_torsion2.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1040SEMIHARMONIC5
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_contact9122SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.32 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2703 147 4.92 %
Rwork0.26 2843 -
all0.2605 2990 -
obs--99.29 %
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)
15.7551-1.1422-2.06696.36692.19474.7896-0.5341-0.5563-1.02750.73580.17780.82310.6355-0.25670.3564-0.48940.02260.1575-0.4978-0.0419-0.210719.848235.02635.3345
23.8656-1.0783-2.00345.53782.22115.99970.17730.3481-0.1304-0.6017-0.0783-0.0114-0.48-0.3496-0.099-0.4220.02030.1006-0.5034-0.19-0.246724.061944.7561-3.317
32.51220.84720.14433.92020.382410.63160.2664-0.00550.3453-0.5153-0.3975-0.1203-1.51640.92660.13110.1312-0.03570.2786-0.593-0.0036-0.427925.681493.614550.4269
41.87160.3579-0.97223.89743.20811.64520.29370.0490.0544-0.5372-0.55840.5792-1.3555-1.24970.2647-0.11060.20340.1541-0.5491-0.1125-0.36314.481588.491453.4232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 73:603
2X-RAY DIFFRACTION2CHAIN B AND RESSEQ 73:332
3X-RAY DIFFRACTION3CHAIN C AND RESSEQ 73:603
4X-RAY DIFFRACTION4CHAIN D AND RESSEQ 73:333

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