[English] 日本語
Yorodumi
- PDB-4bw5: Crystal structure of human two pore domain potassium ion channel ... -

+
Open data


ID or keywords:

Loading...

-
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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
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)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

-
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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more