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- EMDB-24490: Aplysia Slo1 with Barium -

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Basic information

Entry
Database: EMDB / ID: EMD-24490
TitleAplysia Slo1 with Barium
Map data
Sample
  • Complex: Slo1
    • Protein or peptide: BK channel
  • Ligand: BARIUM ION
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: POTASSIUM ION
  • Ligand: water
Keywordsion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


large conductance calcium-activated potassium channel activity / monoatomic ion channel complex / postsynaptic 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 / Calcium-activated potassium channel slowpoke-like RCK domain / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / Voltage-dependent channel domain superfamily / Ion transport domain ...: / Ca2+-activated K+ channel Slowpoke, TrkA_C like domain / Calcium-activated potassium channel BK, alpha subunit / : / Calcium-activated BK potassium channel alpha subunit / Calcium-activated potassium channel slowpoke-like RCK domain / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / 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: 2.93 Å
AuthorsZhu J / Srivastava S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1ZIANS002993 United States
CitationJournal: To Be Published
Title: CryoEM structure of Aplysia Slo1 with 10 mM Ba2+ at 2.93 A
Authors: Zhu J / Srivastava S / Cachau R / Holmgren M
History
DepositionJul 21, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24490.png

Downloads & links

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Map

FileDownload / File: emd_24490.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.14 Å/pix.
x 256 pix.
= 292.897 Å		1.14 Å/pix.
x 256 pix.
= 292.897 Å		1.14 Å/pix.
x 256 pix.
= 292.897 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14413 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-19.147081 - 44.755074
Average (Standard dev.)-0.000000000000663 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 292.89728 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Slo1

EntireName: Slo1
Components
  • Complex: Slo1
    • Protein or peptide: BK channel
  • Ligand: BARIUM ION
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: POTASSIUM ION
  • Ligand: water

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Supramolecule #1: Slo1

SupramoleculeName: Slo1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Aplysia californica (California sea hare)

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Macromolecule #1: BK channel

MacromoleculeName: BK channel / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Aplysia californica (California sea hare)
Molecular weightTheoretical: 121.386211 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 TNHSNFLEVL FQ

UniProtKB: BK channel

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Macromolecule #2: BARIUM ION

MacromoleculeName: BARIUM ION / type: ligand / ID: 2 / Number of copies: 9 / Formula: BA
Molecular weightTheoretical: 137.327 Da

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Macromolecule #3: (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: 3 / Number of copies: 16 / Formula: PGW
Molecular weightTheoretical: 749.007 Da

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Macromolecule #4: POTASSIUM ION

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

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 24 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5
Component:
ConcentrationFormula
20.0 mMTris-HCl
320.0 mMKCl
5.0 mMEGTA
20.0 mMDTT
2.0 mMTCEP
0.025 %DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was in DDM.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 594822
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 5 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5tj6


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7rjt:
Aplysia Slo1 with Barium

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