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- EMDB-34858: ion channel -

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Basic information

Entry
Database: EMDB / ID: EMD-34858
Titleion channel
Map datacomposite map
Sample
  • Complex: ion channel
    • Protein or peptide: Potassium channel subfamily T member 1
  • Ligand: ~{N}-[(1~{S})-1-[3-(2-methoxypyridin-4-yl)-1,2,4-oxadiazol-5-yl]ethyl]-2-methyl-5-(trifluoromethyl)pyrazole-3-carboxamide
  • Ligand: ZINC ION
  • Ligand: POTASSIUM IONPotassium
  • Ligand: SODIUM IONSodium
Keywordsion channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


intracellular sodium-activated potassium channel activity / outward rectifier potassium channel activity / potassium ion transmembrane transport / plasma membrane
Similarity search - Function
: / Calcium-activated potassium channel BK, alpha subunit / Calcium-activated BK potassium channel alpha subunit / Potassium channel domain / Ion channel
Similarity search - Domain/homology
Potassium channel subfamily T member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsJiang DH / Zhang JT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271272 China
CitationJournal: Cell Rep / Year: 2023
Title: Structural basis of human Slo2.2 channel gating and modulation.
Authors: Jiangtao Zhang / Shiqi Liu / Junping Fan / Rui Yan / Bo Huang / Feng Zhou / Tian Yuan / Jianke Gong / Zhuo Huang / Daohua Jiang /
Abstract: The sodium-activated Slo2.2 channel is abundantly expressed in the brain, playing a critical role in regulating neuronal excitability. The Na-binding site and the underlying mechanisms of Na- ...The sodium-activated Slo2.2 channel is abundantly expressed in the brain, playing a critical role in regulating neuronal excitability. The Na-binding site and the underlying mechanisms of Na-dependent activation remain unclear. Here, we present cryoelectron microscopy (cryo-EM) structures of human Slo2.2 in closed, open, and inhibitor-bound form at resolutions of 2.6-3.2 Å, revealing gating mechanisms of Slo2.2 regulation by cations and a potent inhibitor. The cytoplasmic gating ring domain of the closed Slo2.2 harbors multiple K and Zn sites, which stabilize the channel in the closed conformation. The open Slo2.2 structure reveals at least two Na-sensitive sites where Na binding induces expansion and rotation of the gating ring that opens the inner gate. Furthermore, a potent inhibitor wedges into a pocket formed by pore helix and S6 helix and blocks the pore. Together, our results provide a comprehensive structural framework for the investigation of Slo2.2 channel gating, Na sensation, and inhibition.
History
DepositionNov 27, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34858.png

Downloads & links

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Map

FileDownload / File: emd_34858.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.502
Minimum - Maximum-0.3340395 - 3.6984463
Average (Standard dev.)0.035484314 (±0.118136205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: TMD half map A

Fileemd_34858_additional_1.map
AnnotationTMD half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

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Additional map: TMD map

Fileemd_34858_additional_2.map
AnnotationTMD map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: TMD half map B

Fileemd_34858_additional_3.map
AnnotationTMD half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: gating ring map

Fileemd_34858_additional_4.map
Annotationgating ring map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: gating ring half map A

Fileemd_34858_half_map_1.map
Annotationgating ring half map A
Projections & Slices
AxesZYX

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Histogram

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Half map: gating ring half map B

Fileemd_34858_half_map_2.map
Annotationgating ring half map B
Projections & Slices
AxesZYX

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Sample components

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Entire : ion channel

EntireName: ion channel
Components
  • Complex: ion channel
    • Protein or peptide: Potassium channel subfamily T member 1
  • Ligand: ~{N}-[(1~{S})-1-[3-(2-methoxypyridin-4-yl)-1,2,4-oxadiazol-5-yl]ethyl]-2-methyl-5-(trifluoromethyl)pyrazole-3-carboxamide
  • Ligand: ZINC ION
  • Ligand: POTASSIUM IONPotassium
  • Ligand: SODIUM IONSodium

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Supramolecule #1: ion channel

SupramoleculeName: ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Potassium channel subfamily T member 1

MacromoleculeName: Potassium channel subfamily T member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 139.865234 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPLPDGARTP GGVCREARGG GYTNRTFEFD DGQCAPRRPC AGDGALLDTA GFKMSDLDSE VLPLPPRYRF RDLLLGDPSF QNDDRVQVE FYVNENTFKE RLKLFFIKNQ RSSLRIRLFN FSLKLLTCLL YIVRVLLDDP ALGIGCWGCP KQNYSFNDSS S EINWAPIL ...String:
MPLPDGARTP GGVCREARGG GYTNRTFEFD DGQCAPRRPC AGDGALLDTA GFKMSDLDSE VLPLPPRYRF RDLLLGDPSF QNDDRVQVE FYVNENTFKE RLKLFFIKNQ RSSLRIRLFN FSLKLLTCLL YIVRVLLDDP ALGIGCWGCP KQNYSFNDSS S EINWAPIL WVERKMTLWA IQVIVAIISF LETMLLIYLS YKGNIWEQIF RVSFVLEMIN TLPFIITIFW PPLRNLFIPV FL NCWLAKH ALENMINDFH RAILRTQSAM FNQVLILFCT LLCLVFTGTC GIQHLERAGE NLSLLTSFYF CIVTFSTVGY GDV TPKIWP SQLLVVIMIC VALVVLPLQF EELVYLWMER QKSGGNYSRH RAQTEKHVVL CVSSLKIDLL MDFLNEFYAH PRLQ DYYVV ILCPTEMDVQ VRRVLQIPLW SQRVIYLQGS ALKDQDLMRA KMDNGEACFI LSSRNEVDRT AADHQTILRA WAVKD FAPN CPLYVQILKP ENKFHVKFAD HVVCEEECKY AMLALNCICP ATSTLITLLV HTSRGQEGQE SPEQWQRMYG RCSGNE VYH IRMGDSKFFR EYEGKSFTYA AFHAHKKYGV CLIGLKREDN KSILLNPGPR HILAASDTCF YINITKEENS AFIFKQE EK RKKRAFSGQG LHEGPARLPV HSIIASMGTV AMDLQGTEHR PTQSGGGGGG SKLALPTENG SGSRRPSIAP VLELADSS A LLPCDLLSDQ SEDEVTPSDD EGLSVVEYVK GYPPNSPYIG SSPTLCHLLP VKAPFCCLRL DKGCKHNSYE DAKAYGFKN KLIIVSAETA GNGLYNFIVP LRAYYRSRKE LNPIVLLLDN KPDHHFLEAI CCFPMVYYME GSVDNLDSLL QCGIIYADNL VVVDKESTM SAEEDYMADA KTIVNVQTMF RLFPSLSITT ELTHPSNMRF MQFRAKDSYS LALSKLEKRE RENGSNLAFM F RLPFAAGR VFSISMLDTL LYQSFVKDYM ITITRLLLGL DTTPGSGYLC AMKITEGDLW IRTYGRLFQK LCSSSAEIPI GI YRTESHV FSTSEPHDLR AQSQISVNVE DCEDTREVKG PWGSRAGTGG SSQGRHTGGG DPAEHPLLRR KSLQWARRLS RKA PKQAGR AAAAEWISQQ RLSLYRRSER QELSELVKNR MKHLGLPTTG YDEMNDHQNT LSYVLINPPP DTRLEPSDIV YLIR SDPLA HVASSSQSRK SSCSHKLSSC NPETRDETQL

UniProtKB: Potassium channel subfamily T member 1

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Macromolecule #2: ~{N}-[(1~{S})-1-[3-(2-methoxypyridin-4-yl)-1,2,4-oxadiazol-5-yl]e...

MacromoleculeName: ~{N}-[(1~{S})-1-[3-(2-methoxypyridin-4-yl)-1,2,4-oxadiazol-5-yl]ethyl]-2-methyl-5-(trifluoromethyl)pyrazole-3-carboxamide
type: ligand / ID: 2 / Number of copies: 4 / Formula: LQ9
Molecular weightTheoretical: 396.324 Da
Chemical component information

ChemComp-LQ9:
~{N}-[(1~{S})-1-[3-(2-methoxypyridin-4-yl)-1,2,4-oxadiazol-5-yl]ethyl]-2-methyl-5-(trifluoromethyl)pyrazole-3-carboxamide

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 11 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40913

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