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- PDB-4wff: Human TRAAK K+ channel in a K+ bound nonconductive conformation -

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Basic information

Entry
Database: PDB / ID: 4wff
TitleHuman TRAAK K+ channel in a K+ bound nonconductive conformation
Components
  • (ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT ...) x 2
  • Potassium channel subfamily K member 4
KeywordsMETAL TRANSPORT / Mechanosensitive ion channel / two-pore domain potassium ion channel / membrane protein
Function / homology
Function and homology information


mechanosensitive potassium channel activity / TWIK related potassium channel (TREK) / detection of mechanical stimulus involved in sensory perception of touch / Phase 4 - resting membrane potential / temperature-gated cation channel activity / sensory perception of temperature stimulus / potassium channel complex / cellular response to alkaline pH / stabilization of membrane potential / potassium ion leak channel activity ...mechanosensitive potassium channel activity / TWIK related potassium channel (TREK) / detection of mechanical stimulus involved in sensory perception of touch / Phase 4 - resting membrane potential / temperature-gated cation channel activity / sensory perception of temperature stimulus / potassium channel complex / cellular response to alkaline pH / stabilization of membrane potential / potassium ion leak channel activity / cellular response to temperature stimulus / outward rectifier potassium channel activity / cellular response to fatty acid / potassium channel activity / sensory perception of pain / potassium ion transmembrane transport / memory / potassium ion transport / cellular response to mechanical stimulus / identical protein binding / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TRAAK / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle ...Two pore domain potassium channel, TRAAK / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DECANE / : / Potassium channel subfamily K member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBrohawn, S.G. / MacKinnon, R.
CitationJournal: Nature / Year: 2014
Title: Physical mechanism for gating and mechanosensitivity of the human TRAAK K+ channel.
Authors: Brohawn, S.G. / Campbell, E.B. / MacKinnon, R.
History
DepositionSep 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Other
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _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_symmetry / _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 / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _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.ptnr2_symmetry / _struct_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 4
B: Potassium channel subfamily K member 4
D: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN
E: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN
F: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN
G: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,62315
Polymers158,1656
Non-polymers4589
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.666, 138.891, 96.531
Angle α, β, γ (deg.)90.00, 95.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22F
13E
23G

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGARGARGAA28 - 28428 - 284
21ARGARGARGARGBB28 - 28428 - 284
12GLNGLNASNASNDC1 - 2111 - 211
22GLNGLNASNASNFE1 - 2111 - 211
13GLUGLUPROPROED1 - 2151 - 215
23GLUGLUPROPROGF1 - 2151 - 215

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Potassium channel subfamily K member 4 / TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK / Two pore potassium ...TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK / Two pore potassium channel KT4.1 / Two pore K(+) channel KT4.1


Mass: 32569.650 Da / Num. of mol.: 2 / Mutation: N104Q, N108Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK4, TRAAK / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9NYG8

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Antibody , 2 types, 4 molecules DFEG

#2: Antibody ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN


Mass: 23038.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN


Mass: 23474.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Non-polymers , 4 types, 192 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.41 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 50 mM TRIS PH 8.8, 200 mM CaCl2, 27-30% (vol/vol) PEG400
PH range: 8-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→48.1 Å / Num. obs: 68997 / % possible obs: 98.9 % / Redundancy: 10.1 % / Net I/σ(I): 34.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I9W
Resolution: 2.5→48.1 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.94 / SU B: 29.468 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24492 3631 5 %RANDOM
Rwork0.21311 ---
obs0.21473 68997 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.23 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å20 Å23.5 Å2
2---6.82 Å20 Å2
3---8.44 Å2
Refinement stepCycle: 1 / Resolution: 2.5→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10384 0 18 183 10585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0210665
X-RAY DIFFRACTIONr_bond_other_d0.0020.029946
X-RAY DIFFRACTIONr_angle_refined_deg1.0021.95114522
X-RAY DIFFRACTIONr_angle_other_deg0.63322950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93651339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20323.704405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55151690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1431542
X-RAY DIFFRACTIONr_chiral_restr0.0590.21657
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111889
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022415
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5694.5295386
X-RAY DIFFRACTIONr_mcbond_other4.5694.5285385
X-RAY DIFFRACTIONr_mcangle_it6.6986.7886715
X-RAY DIFFRACTIONr_mcangle_other6.6976.7896716
X-RAY DIFFRACTIONr_scbond_it5.5144.9215279
X-RAY DIFFRACTIONr_scbond_other5.5144.9225280
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0167.2277808
X-RAY DIFFRACTIONr_long_range_B_refined12.35743.64244522
X-RAY DIFFRACTIONr_long_range_B_other12.35643.64344523
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A127270.15
12B127270.15
21D112020.1
22F112020.1
31E114670.1
32G114670.1
LS refinement shellResolution: 2.497→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.536 203 -
Rwork0.551 4553 -
obs--87.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.1854-0.8124-3.21780.1760.57024.22110.24980.38460.1765-0.1217-0.0452-0.0236-0.38690.2363-0.20470.5937-0.04650.03350.57840.03610.115844.264-5.83510.095
20.1667-0.06490.52340.1105-0.65257.56820.00260.3814-0.1192-0.2596-0.07020.12140.99810.26420.06761.27890.04970.05671.1333-0.14270.652949.951-20.415-20.775
37.8961-0.7616-1.68588.2754-0.46173.9953-0.46760.6975-1.0391-0.5810.1411-0.02020.6657-0.43540.32650.82230.0812-0.07220.9257-0.1220.178245.668-16.753-6.594
43.6422-0.5478-2.86560.5672-0.19264.47490.22790.46810.1306-0.2305-0.1263-0.198-0.39170.2788-0.10160.5774-0.02490.05430.6528-0.00660.15947.875-10.1557.327
55.2837-0.39270.23283.7572-0.99390.2762-0.38210.05380.23470.01410.43140.01180.0168-0.1752-0.04930.86040.02350.00480.9444-0.05670.774792.149-4.559-4.801
65.5421.65540.79951.6433-0.60167.72760.28580.21640.83910.0015-0.0466-0.7626-0.58740.7594-0.23920.8941-0.06480.22610.8880.07631.196564.37-2.7275.524
74.575-1.65090.09335.4796-0.09775.4143-0.17120.26360.567-0.7595-0.24590.2298-0.7979-0.23230.4170.55150.0245-0.21010.341-0.00110.150714.17816.47627.064
83.59861.4913.78523.90933.23396.41290.12540.43590.2907-0.8054-0.19080.0204-0.31890.33570.06540.62640.1008-0.11370.42970.02450.299212.92746.38746.137
93.35420.42562.63864.6143.08686.19160.1470.48070.3855-0.4665-0.1820.1984-0.44950.39990.0350.63760.0391-0.07420.4791-0.01520.314513.41147.4646.114
103.9722-0.5332-0.12966.58263.39395.2459-0.2109-0.17680.33580.20580.05540.2425-0.00660.31890.15550.18870.0219-0.04540.3275-0.00670.048724.9366.52745.274
111.2012-1.5717-1.33646.61122.92111.80820.0868-0.20170.132-0.2064-0.05790.1603-0.19590.1618-0.02890.33580.0104-0.12730.3973-0.04210.090619.32522.13749.269
127.9259-4.6451-0.25324.74830.81981.81050.0002-0.17870.03540.15920.04180.4895-0.1269-0.0426-0.0420.3828-0.0476-0.01190.387-0.07310.46697.3237.12758.26
134.1251-0.39330.35495.1859-1.59352.4038-0.0344-0.2577-0.30580.23160.0327-0.06940.05790.2070.00170.17920.0667-0.05150.35820.03260.072329.728-34.98442.241
148.76493.93393.72595.37791.45613.64390.15160.7569-0.7453-0.44930.1386-0.07970.52750.1602-0.29020.54320.0916-0.05750.41480.14580.76418.795-63.20743.936
152.33152.6780.90833.26250.76582.46390.1920.1643-0.5490.06330.1672-0.24430.66960.0475-0.35920.78270.0526-0.09830.53510.00641.112311.876-72.05646.651
165.41252.1368-0.67765.5298-0.93463.0466-0.02610.1704-0.1106-0.06070.07240.59260.0441-0.0821-0.04630.20730.0345-0.07170.34980.01970.113511.773-25.2431.134
172.7222.2744-0.97053.4674-0.8381.1299-0.0806-0.1379-0.661-0.00610.0190.140.231-0.15370.06160.24160.0458-0.05270.44050.07830.51995.005-45.08542.035
183.5716-1.12421.59375.8076-5.36017.5752-0.3303-0.3137-0.13540.13540.140.2140.3373-0.40380.19030.3392-0.0172-0.04040.50330.00740.6431-3.539-55.61750.52
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 148
2X-RAY DIFFRACTION2A149 - 219
3X-RAY DIFFRACTION3A220 - 286
4X-RAY DIFFRACTION4B28 - 175
5X-RAY DIFFRACTION5B176 - 197
6X-RAY DIFFRACTION6B198 - 284
7X-RAY DIFFRACTION7D1 - 105
8X-RAY DIFFRACTION8D106 - 157
9X-RAY DIFFRACTION9D158 - 211
10X-RAY DIFFRACTION10E1 - 80
11X-RAY DIFFRACTION11E81 - 137
12X-RAY DIFFRACTION12E138 - 217
13X-RAY DIFFRACTION13F1 - 105
14X-RAY DIFFRACTION14F106 - 188
15X-RAY DIFFRACTION15F189 - 211
16X-RAY DIFFRACTION16G1 - 80
17X-RAY DIFFRACTION17G81 - 172
18X-RAY DIFFRACTION18G173 - 216

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