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- EMDB-22200: Cryo-EM structure of the G protein-gated inward rectifier K+ chan... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22200 | |||||||||
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Title | Cryo-EM structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) in complex with PIP2 | |||||||||
![]() | Cryo-EM structure of the G protein-gated inward rectifier K+ channel GIRK2 | |||||||||
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Function / homology | ![]() 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 / neuronal cell body membrane / potassium ion import across plasma membrane ...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 / neuronal cell body membrane / potassium ion import across plasma membrane / potassium channel activity / G-protein alpha-subunit binding / negative regulation of insulin secretion / presynapse / presynaptic membrane / postsynapse / axon / dendrite / cell surface / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Niu Y / Tao X / MacKinnon R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM analysis of PIP regulation in mammalian GIRK channels. Authors: Yiming Niu / Xiao Tao / Kouki K Touhara / Roderick MacKinnon / ![]() Abstract: G-protein-gated inward rectifier potassium (GIRK) channels are regulated by G proteins and PIP. Here, using cryo-EM single particle analysis we describe the equilibrium ensemble of structures of ...G-protein-gated inward rectifier potassium (GIRK) channels are regulated by G proteins and PIP. Here, using cryo-EM single particle analysis we describe the equilibrium ensemble of structures of neuronal GIRK2 as a function of the C8-PIP concentration. We find that PIP shifts the equilibrium between two distinguishable structures of neuronal GIRK (GIRK2), extended and docked, towards the docked form. In the docked form the cytoplasmic domain, to which G binds, becomes accessible to the cytoplasmic membrane surface where G resides. Furthermore, PIP binding reshapes the G binding surface on the cytoplasmic domain, preparing it to receive G. We find that cardiac GIRK (GIRK1/4) can also exist in both extended and docked conformations. These findings lead us to conclude that PIP influences GIRK channels in a structurally similar manner to Kir2.2 channels. In Kir2.2 channels, the PIP-induced conformational changes open the pore. In GIRK channels, they prepare the channel for activation by G. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 229.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.1 KB 14.1 KB | Display Display | ![]() |
Images | ![]() | 31.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xitMC ![]() 6xisC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM structure of the G protein-gated inward rectifier K+ channel GIRK2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Homo-tetrameric assembly of G protein-activated inward rectifier ...
Entire | Name: Homo-tetrameric assembly of G protein-activated inward rectifier potassium channel 2 |
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Components |
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-Supramolecule #1: Homo-tetrameric assembly of G protein-activated inward rectifier ...
Supramolecule | Name: Homo-tetrameric assembly of G protein-activated inward rectifier potassium channel 2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: G protein-activated inward rectifier potassium channel 2
Macromolecule | Name: G protein-activated inward rectifier potassium channel 2 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 39.061957 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MAKRKIQRYV RKDGKCNVHH GNVRETYRYL TDIFTTLVDL KWRFNLLIFV MVYTVTWLFF GMIWWLIAYI RGDMDHIEDP SWTPCVTNL NGFVSAFLFS IETETTIGYG YRVITDKCPE GIILLLIQSV LGSIVNAFMV GCMFVKISQP KKRAETLVFS T HAVISMRD ...String: MAKRKIQRYV RKDGKCNVHH GNVRETYRYL TDIFTTLVDL KWRFNLLIFV MVYTVTWLFF GMIWWLIAYI RGDMDHIEDP SWTPCVTNL NGFVSAFLFS IETETTIGYG YRVITDKCPE GIILLLIQSV LGSIVNAFMV GCMFVKISQP KKRAETLVFS T HAVISMRD GKLCLMFRVG DLRNSHIVEA SIRAKLIKSK QTSEGEFIPL NQTDINVGYY TGDDRLFLVS PLIISHEINQ QS PFWEISK AQLPKEELEI VVILEGMVEA TGMTCQARSS YITSEILWGY RFTPVLTLED GFYEVDYNSF HETYETSTPS LSA KELAEL ANRAESNSLE VLFQ |
-Macromolecule #2: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...
Macromolecule | Name: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate type: ligand / ID: 2 / Number of copies: 4 / Formula: PIO |
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Molecular weight | Theoretical: 746.566 Da |
Chemical component information | ![]() ChemComp-PIO: |
-Macromolecule #3: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL |
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Buffer | pH: 7.5 Details: 20 mM Tris-HCl pH 7.5, 150 mM KCl, 10 mM DTT, 1 mM DETA, 0.2% DM and 0.01% CHS |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 11349 / Average exposure time: 10.0 sec. / Average electron dose: 8.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |