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- EMDB-33977: Cryo-EM structure of human Slo1-LRRC26 complex with Symmetry Expansion -

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Basic information

Entry
Database: EMDB / ID: EMD-33977
TitleCryo-EM structure of human Slo1-LRRC26 complex with Symmetry Expansion
Map data
Sample
  • Complex: human Slo1-LRRC26 complex
    • Protein or peptide: Calcium-activated potassium channel subunit alpha-1
    • Protein or peptide: Leucine-rich repeat-containing protein 26
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


positive regulation of voltage-gated potassium channel activity / monoatomic ion-gated channel activity / potassium channel activator activity / ligand-gated monoatomic cation channel activity / voltage-gated potassium channel activity / potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / transmembrane transporter binding ...positive regulation of voltage-gated potassium channel activity / monoatomic ion-gated channel activity / potassium channel activator activity / ligand-gated monoatomic cation channel activity / voltage-gated potassium channel activity / potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / transmembrane transporter binding / cytoskeleton / extracellular exosome / membrane / plasma membrane / cytoplasm
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 / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...: / : / 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 / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ion transport domain / Ion transport protein / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Calcium-activated potassium channel subunit alpha-1 / Leucine-rich repeat-containing protein 26
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYamanouchi D / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Structural basis for dual allosteric gating modulation of Slo1-LRRC channel complex
Authors: Yamanouchi D
History
DepositionAug 1, 2022-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33977.png

Downloads & links

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Map

FileDownload / File: emd_33977.map.gz / Format: CCP4 / Size: 103 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 Å/pix.
x 300 pix.
= 298.8 Å		1 Å/pix.
x 300 pix.
= 298.8 Å		1 Å/pix.
x 300 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.996 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0191
Minimum - Maximum-0.06866419 - 0.13048087
Average (Standard dev.)0.0003802897 (±0.0039883414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33977_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33977_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33977_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : human Slo1-LRRC26 complex

EntireName: human Slo1-LRRC26 complex
Components
  • Complex: human Slo1-LRRC26 complex
    • Protein or peptide: Calcium-activated potassium channel subunit alpha-1
    • Protein or peptide: Leucine-rich repeat-containing protein 26
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION

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Supramolecule #1: human Slo1-LRRC26 complex

SupramoleculeName: human Slo1-LRRC26 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 616 kDa/nm

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Macromolecule #1: Calcium-activated potassium channel subunit alpha-1

MacromoleculeName: Calcium-activated potassium channel subunit alpha-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 119.4585 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDALIIPVTM EVPCDSRGQR MWWAFLASSM VTFFGGLFII LLWRTLKYLW TVCCHCGGKT KEAQKINNGS SQADGTLKPV DEKEEAVAA EVGWMTSVKD WAGVMISAQT LTGRVLVVLV FALSIGALVI YFIDSSNPIE SCQNFYKDFT LQIDMAFNVF F LLYFGLRF ...String:
MDALIIPVTM EVPCDSRGQR MWWAFLASSM VTFFGGLFII LLWRTLKYLW TVCCHCGGKT KEAQKINNGS SQADGTLKPV DEKEEAVAA EVGWMTSVKD WAGVMISAQT LTGRVLVVLV FALSIGALVI YFIDSSNPIE SCQNFYKDFT LQIDMAFNVF F LLYFGLRF IAANDKLWFW LEVNSVVDFF TVPPVFVSVY LNRSWLGLRF LRALRLIQFS EILQFLNILK TSNSIKLVNL LS IFISTWL TAAGFIHLVE NSGDPWENFQ NNQALTYWEC VYLLMVTMST VGYGDVYAKT TLGRLFMVFF ILGGLAMFAS YVP EIIELI GNRKKYGGSY SAVSGRKHIV VCGHITLESV SNFLKDFLHK DRDDVNVEIV FLHNISPNLE LEALFKRHFT QVEF YQGSV LNPHDLARVK IESADACLIL ANKYCADPDA EDASNIMRVI SIKNYHPKIR IITQMLQYHN KAHLLNIPSW NWKEG DDAI CLAELKLGFI AQSCLAQGLS TMLANLFSMR SFIKIEEDTW QKYYLEGVSN EMYTEYLSSA FVGLSFPTVC ELCFVK LKL LMIAIEYKSA NRESRSRSRI LINPGNHLKI QEGTLGFFIA SDAKEVKRAF FYCKACHDDI TDPKRIKKCG CKRLEDE QP STLSPKKKQR NGGMRNSPNT SPKLMRHDPL LIPGNDQIDN MDSNVKKYDS TGMFHWCAPK EIEKVILTRS EAAMTVLS G HVVVCIFGDV SSALIGLRNL VMPLRASNFH YHELKHIVFV GSIEYLKREW ETLHNFPKVS ILPGTPLSRA DLRAVNINL CDMCVILSAN QNNIDDTSLQ DKECILASLN IKSMQFDDSI GVLQANSQGF TPPGMDRSSP DNSPVHGMLR QPSITTGVNI PIITELVND TNVQFLDQDD DDDPDTELYL TQPFACGTAF AVSVLDSLMS ATYFNDNILT LIRTLVTGGA TPELEALIAE E NALRGGYS TPQTLANRDR CRVAQLALLD GPFADLGDGG CYGDLFCKAL KTYNMLCFGI YRLRDAHLST PSQCTKRYVI TN PPYEFEL VPTDLIFCLM QFD

UniProtKB: Calcium-activated potassium channel subunit alpha-1

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Macromolecule #2: Leucine-rich repeat-containing protein 26

MacromoleculeName: Leucine-rich repeat-containing protein 26 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.893629 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRGPSWSRPR PLLLLLLLLS PWPVWAQVSA TASPSGSLGA PDCPEVCTCV PGGLASCSAL SLPAVPPGLS LRLRALLLDH NRVRALPPG AFAGAGALQR LDLRENGLHS VHVRAFWGLG ALQLLDLSAN QLEALAPGTF APLRALRNLS LAGNRLARLE P AALGALPL ...String:
MRGPSWSRPR PLLLLLLLLS PWPVWAQVSA TASPSGSLGA PDCPEVCTCV PGGLASCSAL SLPAVPPGLS LRLRALLLDH NRVRALPPG AFAGAGALQR LDLRENGLHS VHVRAFWGLG ALQLLDLSAN QLEALAPGTF APLRALRNLS LAGNRLARLE P AALGALPL LRSLSLQDNE LAALAPGLLG RLPALDALHL RGNPWGCGCA LRPLCAWLRR HPLPASEAET VLCVWPGRLT LS PLTAFSD AAFSHCAQPL ALRDLAVVYT LGPASFLVSL ASCLALGSGL TACRARRRRL RTAALRPPRP PDPNPDPDPH GCA SPADPG SPAAAAQA

UniProtKB: Leucine-rich repeat-containing protein 26

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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: 4 / Formula: PGW
Molecular weightTheoretical: 749.007 Da

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 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

Concentration2.0 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46779
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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