[English] 日本語
Yorodumi
- PDB-2qks: Crystal structure of a Kir3.1-prokaryotic Kir channel chimera -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qks
TitleCrystal structure of a Kir3.1-prokaryotic Kir channel chimera
ComponentsKir3.1-prokaryotic Kir channel chimera
KeywordsMETAL TRANSPORT / CHIMERA / G-PROTEIN GATED INWARD RECTIFIER / POTASSIUM CHANNEL / SELECTIVITY FILTER
Function / homology
Function and homology information


I(KACh) inward rectifier potassium channel complex / G-protein activated inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / monoatomic ion channel complex / potassium ion import across plasma membrane ...I(KACh) inward rectifier potassium channel complex / G-protein activated inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / monoatomic ion channel complex / potassium ion import across plasma membrane / response to electrical stimulus / T-tubule / potassium ion transmembrane transport / presynaptic membrane / external side of plasma membrane / cell surface / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir3.1 / G protein-activated inward rectifier potassium channel 1 / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Helix Hairpins - #70 / Potassium channel domain ...Potassium channel, inwardly rectifying, Kir3.1 / G protein-activated inward rectifier potassium channel 1 / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / G protein-activated inward rectifier potassium channel 1 / Inward rectifier potassium channel
Similarity search - Component
Biological speciesMus musculus (house mouse)
Paraburkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNishida, M. / MacKinnon, R.
CitationJournal: Embo J. / Year: 2007
Title: Crystal structure of a Kir3.1-prokaryotic Kir channel chimera.
Authors: Nishida, M. / Cadene, M. / Chait, B.T. / Mackinnon, R.
History
DepositionJul 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Jun 7, 2017Group: Database references / Other / Source and taxonomy
Revision 1.4Jul 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_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr1_symmetry / _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_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 30, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kir3.1-prokaryotic Kir channel chimera
B: Kir3.1-prokaryotic Kir channel chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,12915
Polymers72,3532
Non-polymers77613
Water4,071226
1
A: Kir3.1-prokaryotic Kir channel chimera
hetero molecules

A: Kir3.1-prokaryotic Kir channel chimera
hetero molecules

A: Kir3.1-prokaryotic Kir channel chimera
hetero molecules

A: Kir3.1-prokaryotic Kir channel chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,02736
Polymers144,7064
Non-polymers2,32032
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
2
B: Kir3.1-prokaryotic Kir channel chimera
hetero molecules

B: Kir3.1-prokaryotic Kir channel chimera
hetero molecules

B: Kir3.1-prokaryotic Kir channel chimera
hetero molecules

B: Kir3.1-prokaryotic Kir channel chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,48824
Polymers144,7064
Non-polymers78220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Unit cell
Length a, b, c (Å)98.416, 98.416, 92.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-401-

K

21A-402-

K

31A-403-

K

41A-404-

K

51A-405-

K

61A-406-

K

71A-407-

K

81B-408-

K

91B-409-

K

101B-410-

K

111B-411-

K

121B-412-

K

131A-528-

HOH

141A-530-

HOH

151B-486-

HOH

161B-489-

HOH

DetailsThe biological tetrameric assembly of the chain A molecule is generated by the operations: (y, 1-x, z), (1-x, 1-y, z) and (1-y, x, z). The biological tetrameric assembly of the chain B molecule is generated by the operations: (1-y, -1+x, z), (2-x, -y, z) and (1+y, 1-x, z).

-
Components

#1: Protein Kir3.1-prokaryotic Kir channel chimera / GIRK1 / Potassium channel / inwardly rectifying subfamily J member 3 / Inward rectifier K+ / channel Kir3.1


Mass: 36176.582 Da / Num. of mol.: 2
Fragment: KIR3.1 (residues 3-44, 125-318), KIRBAC1.3 TRANSMEMBRANE domain (residues 45-124)
Mutation: M127A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Paraburkholderia xenovorans (bacteria)
Genus: Burkholderia / Plasmid: pET28b(+) / Strain: LB400 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63250, UniProt: Q146M9
#2: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 10-15% (w/v) PEG 4000, 0.05M sodium citrate, 0.2M potassium phosphate, 0.08M bis-tris, 0.12M KCl, 0.003M dithiothreitol, 0.02M tris (2-carboxyethyl) phosphine hydrochloride, 0.0026M 1,2- ...Details: 10-15% (w/v) PEG 4000, 0.05M sodium citrate, 0.2M potassium phosphate, 0.08M bis-tris, 0.12M KCl, 0.003M dithiothreitol, 0.02M tris (2-carboxyethyl) phosphine hydrochloride, 0.0026M 1,2-dihexanoyl phosphatidylinositol 4,5-biphosphate, 0.016M nonylglucoside , pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2006
RadiationMonochromator: DOUBLE CRYSTALS (Silicon) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 43991 / Num. obs: 43991 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 46.1 Å2 / Rsym value: 0.054 / Net I/σ(I): 17
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 4450 / Rsym value: 0.309 / % possible all: 99.7

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1N9P, 1P7B

1n9p

1p7b


Resolution: 2.2→29.5 Å
Isotropic thermal model: Anisotropic model for the reflection data and restrained individual isotoropic temperature factors for the coordinates
Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: During the refinement, only the anisotropic components of the correction were applied to the data, the isotropic component was not applied to the coordinates. The bulk solvent correction was ...Details: During the refinement, only the anisotropic components of the correction were applied to the data, the isotropic component was not applied to the coordinates. The bulk solvent correction was applied between 5-2.2 A. Potassium ions are located using another crystal soaked in a rubidium-containing solution.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2179 -RANDOM
Rwork0.231 ---
all0.232 43987 --
obs0.232 43987 97.9 %-
Displacement parametersBiso mean: 51.229 Å2
Baniso -1Baniso -2Baniso -3
1--1.324 Å20 Å20 Å2
2---1.324 Å20 Å2
3---2.648 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4660 0 33 226 4919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it1.58
X-RAY DIFFRACTIONc_mcangle_it2.68
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.87
LS refinement shellResolution: 2.2→2.37 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.327 452 -
Rwork0.287 --
obs-8902 99.6 %

+
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