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- EMDB-8410: Ca2+ bound aplysia Slo1 -

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Basic information

Entry
Database: EMDB / ID: EMD-8410
TitleCa2+ bound aplysia Slo1
Map dataMg and Ca-bound aplysia Slo1
Sample
  • Organelle or cellular component: Ca2+ bound aplysia Slo1
    • Protein or peptide: High conductance calcium-activated potassium channel
  • Ligand: POTASSIUM IONPotassium
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM IONCalcium
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
Keywordsion channel / K+ channel / Ca2+ bound / high conductance / MEMBRANE PROTEIN
Function / homology
Function and homology information


potassium ion transport / monoatomic ion channel activity / membrane
Similarity search - Function
: / Ca2+-activated K+ channel Slowpoke, TrkA_C like domain / : / Calcium-activated potassium channel BK, alpha subunit / Calcium-activated BK potassium channel alpha subunit / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesAplysia californica (California sea hare)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMacKinnon R / Tao X
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM43949 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2017
Title: Cryo-EM structure of the open high-conductance Ca-activated K channel.
Authors: Xiao Tao / Richard K Hite / Roderick MacKinnon /
Abstract: The Ca-activated K channel, Slo1, has an unusually large conductance and contains a voltage sensor and multiple chemical sensors. Dual activation by membrane voltage and Ca renders Slo1 central to ...The Ca-activated K channel, Slo1, has an unusually large conductance and contains a voltage sensor and multiple chemical sensors. Dual activation by membrane voltage and Ca renders Slo1 central to processes that couple electrical signalling to Ca-mediated events such as muscle contraction and neuronal excitability. Here we present the cryo-electron microscopy structure of a full-length Slo1 channel from Aplysia californica in the presence of Ca and Mg at a resolution of 3.5 Å. The channel adopts an open conformation. Its voltage-sensor domain adopts a non-domain-swapped attachment to the pore and contacts the cytoplasmic Ca-binding domain from a neighbouring subunit. Unique structural features of the Slo1 voltage sensor suggest that it undergoes different conformational changes than other known voltage sensors. The structure reveals the molecular details of three distinct divalent cation-binding sites identified through electrophysiological studies of mutant Slo1 channels.
History
DepositionOct 3, 2016-
Header (metadata) releaseNov 16, 2016-
Map releaseJan 11, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5tj6
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8410.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMg and Ca-bound aplysia Slo1
Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.018576425 - 0.049764723
Average (Standard dev.)-0.00023435285 (±0.002291491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0190.050-0.000

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Supplemental data

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Sample components

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Entire : Ca2+ bound aplysia Slo1

EntireName: Ca2+ bound aplysia Slo1
Components
  • Organelle or cellular component: Ca2+ bound aplysia Slo1
    • Protein or peptide: High conductance calcium-activated potassium channel
  • Ligand: POTASSIUM IONPotassium
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM IONCalcium
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

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Supramolecule #1: Ca2+ bound aplysia Slo1

SupramoleculeName: Ca2+ bound aplysia Slo1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Aplysia californica (California sea hare)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: High conductance calcium-activated potassium channel

MacromoleculeName: High conductance calcium-activated potassium channel / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aplysia californica (California sea hare)
Molecular weightTheoretical: 120.308 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASSSSTSCE PGDRQWYSFL ASSLVTFGSG LVVIIIYRIV LWLCCRKKKC IQVSNPVPTA RTTSLDQKSF MKNSDPEIGW MTEAKDWAG ELISGQTTTG RILVGLVFLL SIASLIIYFI DASTNTSVET CLPWSSSTTQ QVDLAFNVFF MIYFFIRFVA A NDKLWFWV ...String:
MASSSSTSCE PGDRQWYSFL ASSLVTFGSG LVVIIIYRIV LWLCCRKKKC IQVSNPVPTA RTTSLDQKSF MKNSDPEIGW MTEAKDWAG ELISGQTTTG RILVGLVFLL SIASLIIYFI DASTNTSVET CLPWSSSTTQ QVDLAFNVFF MIYFFIRFVA A NDKLWFWV ELFSFVDYFT IPPSFVAIYL DRNWLGLRFL RALRLMSIPD ILTYLNVLKT STLIRLVQLV VSFVSLWLTA AG FLHLLEN SGDPFFDFGN AQHLTYWECL YFLMVTMSTV GFGDIFATTV LGRTFVVIFI MIFIGLFASF IPEIAEILGK RQK YGGSYK KERGKRHVVV CGYITFDSVS NFLKDFLHKD REDVDVEIVF LHKGLPGLEL EGLLKRHFTQ VEYFWGSVMD ANDL ERVKI QEADACLVLA NKYCQDPDQE DAANIMRVIS IKNYHSDIKV IVQLLQYHNK AYLLNIPSWD WKRGDDAVCV AELKL GFIA QSCLAPGFST LMANLFTMRS YKPTPEMSQW QTDYMRGTGM EMYTEYLSSA FNALTFPEAA ELCFSKLKLL LLAIEV RQE DTRESTLAIN PGPKVKIENA TQGFFIAESA EEVKRAFYYC KNCHANVSDV RQIKKCKCRP LAMFKKGAAA VLALQRT PG LAVEPDGEAN DKDKSRGTST SKAVTSFPEK RKPQSRRKPS TTLKSKSPSE DSVPPPPPPV DEPRKFDSTG MFHWCPDR P LNDCLQDRSQ ASASGLRNHV VVCLFADAAS PLIGLRNLVM PLRASNFHYH ELKPTIIVGN LDYLHREWKT LQNFPKLSI LPGSPLNRAN LRAVNINLCD MCVIVSAKDR NMEDPNLVDK EAILCSLNIK AMTFDDTMGL IQSSNFVPGG FSPLHENKRS QAGANVPLI TELANDSNVQ FLDQDDDDDP DTELYMTQPF ACGTAFAVSV LDSLMSTSYF NDNALTLIRT LITGGATPEL E QILAEGAG MRGGYCSPAV LANRDRCRVA QISLFDGPLA QFGQGGHYGE LFVYALRHFG ILCIGLYRFR DTNESVRSPS SK RYVITNP PEDFPLLPTD QVYVLTYKQI TNH

UniProtKB: BK channel

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 5 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...

MacromoleculeName: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
type: ligand / ID: 5 / Number of copies: 15 / Formula: PGW
Molecular weightTheoretical: 749.007 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

Concentration7 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTrisTris
320.0 mMKClKCl
10.0 mMCaCl2CaCl2
10.0 mMMgCl2MgCl2
20.0 mMDTTDTT
2.0 mMTCEPTCEP
0.025 %DDMDDM
0.005 %CHSCHS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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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 / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 2000 / Average exposure time: 0.3 sec. / Average electron dose: 1.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 233000
Startup modelType of model: OTHER
Details: An initial model generated from 2D class averages in EMAN2
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 115000

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 100
Output model

PDB-5tj6:
Ca2+ bound aplysia Slo1

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