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- EMDB-34827: potassium channels -

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Basic information

Entry
Database: EMDB / ID: EMD-34827
Titlepotassium channels
Map data
Sample
  • Complex: potassium channel
    • Protein or peptide: Potassium channel subfamily T member 1
  • Ligand: SODIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: ZINC ION
Keywordspotassium channels / 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 / Calcium-activated potassium channel slowpoke-like RCK domain / RCK N-terminal domain profile. / 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: 3.18 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 21, 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_34827.png

Downloads & links

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Map

FileDownload / File: emd_34827.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.771
Minimum - Maximum-2.0591583 - 3.584652
Average (Standard dev.)0.007238213 (±0.13301519)
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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Half map: #2

Fileemd_34827_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34827_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : potassium channel

EntireName: potassium channel
Components
  • Complex: potassium channel
    • Protein or peptide: Potassium channel subfamily T member 1
  • Ligand: SODIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: ZINC ION

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Supramolecule #1: potassium channel

SupramoleculeName: potassium 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: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #4: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...

MacromoleculeName: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
type: ligand / ID: 4 / Number of copies: 4 / Formula: 6OU
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28867
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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