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- EMDB-22425: Rabbit Cav1.1 in the presence of 100 micromolar (R)-(+)-Bay K8644... -

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Basic information

Entry
Database: EMDB / ID: EMD-22425
TitleRabbit Cav1.1 in the presence of 100 micromolar (R)-(+)-Bay K8644 in nanodiscs at 3.2 Angstrom resolution
Map data
Sample
  • Complex: rCav1.1-100R
    • Protein or peptide: Voltage-dependent L-type calcium channel subunit alpha-1S
    • Protein or peptide: Voltage-dependent calcium channel gamma-1 subunit
    • Protein or peptide: Voltage-dependent calcium channel subunit alpha-2/delta-1
  • Ligand: CALCIUM ION
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: methyl (4~{R})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyridine-3-carboxylate
KeywordsrCav1.1 / Channels / Calcium Ion-Selective / TRANSPORT PROTEIN / drugs
Function / homology
Function and homology information


positive regulation of muscle contraction / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / calcium ion import across plasma membrane / cellular response to caffeine / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol ...positive regulation of muscle contraction / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / calcium ion import across plasma membrane / cellular response to caffeine / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / muscle contraction / T-tubule / calcium ion transmembrane transport / sarcolemma / transmembrane transporter binding / calmodulin binding / metal ion binding / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, gamma-1 subunit / Voltage-dependent calcium channel, L-type, alpha-1S subunit / PMP-22/EMP/MP20/Claudin tight junction / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / VWA N-terminal / Voltage-dependent calcium channel, alpha-2/delta subunit, conserved region / : / VWA N-terminal ...Voltage-dependent calcium channel, gamma-1 subunit / Voltage-dependent calcium channel, L-type, alpha-1S subunit / PMP-22/EMP/MP20/Claudin tight junction / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / VWA N-terminal / Voltage-dependent calcium channel, alpha-2/delta subunit, conserved region / : / VWA N-terminal / Neuronal voltage-dependent calcium channel alpha 2acd / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / : / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / Voltage-dependent channel domain superfamily / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Voltage-dependent L-type calcium channel subunit alpha-1S / Voltage-dependent calcium channel subunit alpha-2/delta-1 / Voltage-dependent calcium channel gamma-1 subunit
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYan N / Gao S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1420541 United States
CitationJournal: Angew Chem Int Ed Engl / Year: 2021
Title: Structural Basis of the Modulation of the Voltage-Gated Calcium Ion Channel Ca 1.1 by Dihydropyridine Compounds*.
Authors: Shuai Gao / Nieng Yan /
Abstract: 1,4-Dihydropyridines (DHP), the most commonly used antihypertensives, function by inhibiting the L-type voltage-gated Ca (Ca ) channels. DHP compounds exhibit chirality-specific antagonistic or ...1,4-Dihydropyridines (DHP), the most commonly used antihypertensives, function by inhibiting the L-type voltage-gated Ca (Ca ) channels. DHP compounds exhibit chirality-specific antagonistic or agonistic effects. The structure of rabbit Ca 1.1 bound to an achiral drug nifedipine reveals the general binding mode for DHP drugs, but the molecular basis for chiral specificity remained elusive. Herein, we report five cryo-EM structures of nanodisc-embedded Ca 1.1 in the presence of the bestselling drug amlodipine, a DHP antagonist (R)-(+)-Bay K8644, and a titration of its agonistic enantiomer (S)-(-)-Bay K8644 at resolutions of 2.9-3.4 Å. The amlodipine-bound structure reveals the molecular basis for the high efficacy of the drug. All structures with the addition of the Bay K8644 enantiomers exhibit similar inactivated conformations, suggesting that (S)-(-)-Bay K8644, when acting as an agonist, is insufficient to lock the activated state of the channel for a prolonged duration.
History
DepositionAug 10, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jpw
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22425.png

Downloads & links

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Map

FileDownload / File: emd_22425.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 280 pix.
= 311.92 Å		1.11 Å/pix.
x 280 pix.
= 311.92 Å		1.11 Å/pix.
x 280 pix.
= 311.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.114 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.08895473 - 0.1448058
Average (Standard dev.)-0.0000027119963 (±0.0038986073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 311.91998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1141.1141.114
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z311.920311.920311.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0890.145-0.000

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Supplemental data

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Sample components

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Entire : rCav1.1-100R

EntireName: rCav1.1-100R
Components
  • Complex: rCav1.1-100R
    • Protein or peptide: Voltage-dependent L-type calcium channel subunit alpha-1S
    • Protein or peptide: Voltage-dependent calcium channel gamma-1 subunit
    • Protein or peptide: Voltage-dependent calcium channel subunit alpha-2/delta-1
  • Ligand: CALCIUM ION
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: methyl (4~{R})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyridine-3-carboxylate

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Supramolecule #1: rCav1.1-100R

SupramoleculeName: rCav1.1-100R / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Voltage-dependent L-type calcium channel subunit alpha-1S

MacromoleculeName: Voltage-dependent L-type calcium channel subunit alpha-1S
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 212.240594 KDa
SequenceString: MEPSSPQDEG LRKKQPKKPL PEVLPRPPRA LFCLTLQNPL RKACISIVEW KPFETIILLT IFANCVALAV YLPMPEDDNN SLNLGLEKL EYFFLTVFSI EAAMKIIAYG FLFHQDAYLR SGWNVLDFII VFLGVFTAIL EQVNVIQSNT APMSSKGAGL D VKALRAFR ...String:
MEPSSPQDEG LRKKQPKKPL PEVLPRPPRA LFCLTLQNPL RKACISIVEW KPFETIILLT IFANCVALAV YLPMPEDDNN SLNLGLEKL EYFFLTVFSI EAAMKIIAYG FLFHQDAYLR SGWNVLDFII VFLGVFTAIL EQVNVIQSNT APMSSKGAGL D VKALRAFR VLRPLRLVSG VPSLQVVLNS IFKAMLPLFH IALLVLFMVI IYAIIGLELF KGKMHKTCYY IGTDIVATVE NE KPSPCAR TGSGRPCTIN GSECRGGWPG PNHGITHFDN FGFSMLTVYQ CITMEGWTDV LYWVNDAIGN EWPWIYFVTL ILL GSFFIL NLVLGVLSGE FTKEREKAKS RGTFQKLREK QQLEEDLRGY MSWITQGEVM DVEDLREGKL SLEEGGSDTE SLYE IEGLN KIIQFIRHWR QWNRVFRWKC HDLVKSRVFY WLVILIVALN TLSIASEHHN QPLWLTHLQD IANRVLLSLF TIEML LKMY GLGLRQYFMS IFNRFDCFVV CSGILELLLV ESGAMTPLGI SVLRCIRLLR LFKITKYWTS LSNLVASLLN SIRSIA SLL LLLFLFIIIF ALLGMQLFGG RYDFEDTEVR RSNFDNFPQA LISVFQVLTG EDWNSVMYNG IMAYGGPSYP GVLVCIY FI ILFVCGNYIL LNVFLAIAVD NLAEAESLTS AQKAKAEERK RRKMSRGLPD KTEEEKSVMA KKLEQKPKGE GIPTTAKL K VDEFESNVNE VKDPYPSADF PGDDEEDEPE IPVSPRPRPL AELQLKEKAV PIPEASSFFI FSPTNKVRVL CHRIVNATW FTNFILLFIL LSSAALAAED PIRAESVRNQ ILGYFDIAFT SVFTVEIVLK MTTYGAFLHK GSFCRNYFNI LDLLVVAVSL ISMGLESST ISVVKILRVL RVLRPLRAIN RAKGLKHVVQ CVFVAIRTIG NIVLVTTLLQ FMFACIGVQL FKGKFFSCND L SKMTEEEC RGYYYVYKDG DPTQMELRPR QWIHNDFHFD NVLSAMMSLF TVSTFEGWPQ LLYRAIDSNE EDMGPVYNNR VE MAIFFII YIILIAFFMM NIFVGFVIVT FQEQGETEYK NCELDKNQRQ CVQYALKARP LRCYIPKNPY QYQVWYVVTS SYF EYLMFA LIMLNTICLG MQHYHQSEEM NHISDILNVA FTIIFTLEMI LKLLAFKARG YFGDPWNVFD FLIVIGSIID VILS EIDTF LASSGGLYCL GGGCGNVDPD ESARISSAFF RLFRVMRLIK LLSRAEGVRT LLWTFIKSFQ ALPYVALLIV MLFFI YAVI GMQMFGKIAL VDGTQINRNN NFQTFPQAVL LLFRCATGEA WQEILLACSY GKLCDPESDY APGEEYTCGT NFAYYY FIS FYMLCAFLII NLFVAVIMDN FDYLTRDWSI LGPHHLDEFK AIWAEYDPEA KGRIKHLDVV TLLRRIQPPL GFGKFCP HR VACKRLVGMN MPLNSDGTVT FNATLFALVR TALKIKTEGN FEQANEELRA IIKKIWKRTS MKLLDQVIPP IGDDEVTV G KFYATFLIQE HFRKFMKRQE EYYGYRPKKD TVQIQAGLRT IEEEAAPEIR RTISGDLTAE EELERAMVEA AMEERIFRR TGGLFGQVDT FLERTNSLPP VMANQRPLQF AEIEMEELES PVFLEDFPQD ARTNPLARAN TNNANANVAY GNSNHSNNQM FSSVHCERE FPGEAETPAA GRGALSHSHR ALGPHSKPCA GKLNGQLVQP GMPINQAPPA PCQQPSTDPP ERGQRRTSLT G SLQDEAPQ RRSSEGSTPR RPAPATALLI QEALVRGGLD TLAADAGFVT ATSQALADAC QMEPEEVEVA ATELLKARES VQ GMASVPG SLSRRSSLGS LDQVQGSQET LIPPRP

UniProtKB: Voltage-dependent L-type calcium channel subunit alpha-1S

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Macromolecule #2: Voltage-dependent calcium channel gamma-1 subunit

MacromoleculeName: Voltage-dependent calcium channel gamma-1 subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 25.082254 KDa
SequenceString: MSPTEAPKVR VTLFCILVGI VLAMTAVVSD HWAVLSPHME NHNTTCEAAH FGLWRICTKR IALGEDRSCG PITLPGEKNC SYFRHFNPG ESSEIFEFTT QKEYSISAAA ISVFSLGFLI MGTICALMAF RKKRDYLLRP ASMFYVFAGL CLFVSLEVMR Q SVKRMIDS ...String:
MSPTEAPKVR VTLFCILVGI VLAMTAVVSD HWAVLSPHME NHNTTCEAAH FGLWRICTKR IALGEDRSCG PITLPGEKNC SYFRHFNPG ESSEIFEFTT QKEYSISAAA ISVFSLGFLI MGTICALMAF RKKRDYLLRP ASMFYVFAGL CLFVSLEVMR Q SVKRMIDS EDTVWIEYYY SWSFACACAA FVLLFLGGIS LLLFSLPRMP QNPWESCMDA EPEH

UniProtKB: Voltage-dependent calcium channel gamma-1 subunit

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Macromolecule #3: Voltage-dependent calcium channel subunit alpha-2/delta-1

MacromoleculeName: Voltage-dependent calcium channel subunit alpha-2/delta-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 125.082906 KDa
SequenceString: MAAGRPLAWT LTLWQAWLIL IGPSSEEPFP SAVTIKSWVD KMQEDLVTLA KTASGVHQLV DIYEKYQDLY TVEPNNARQL VEIAARDIE KLLSNRSKAL VRLALEAEKV QAAHQWREDF ASNEVVYYNA KDDLDPEKND SEPGSQRIKP VFIDDANFRR Q VSYQHAAV ...String:
MAAGRPLAWT LTLWQAWLIL IGPSSEEPFP SAVTIKSWVD KMQEDLVTLA KTASGVHQLV DIYEKYQDLY TVEPNNARQL VEIAARDIE KLLSNRSKAL VRLALEAEKV QAAHQWREDF ASNEVVYYNA KDDLDPEKND SEPGSQRIKP VFIDDANFRR Q VSYQHAAV HIPTDIYEGS TIVLNELNWT SALDDVFKKN REEDPSLLWQ VFGSATGLAR YYPASPWVDN SRTPNKIDLY DV RRRPWYI QGAASPKDML ILVDVSGSVS GLTLKLIRTS VSEMLETLSD DDFVNVASFN SNAQDVSCFQ HLVQANVRNK KVL KDAVNN ITAKGITDYK KGFSFAFEQL LNYNVSRANC NKIIMLFTDG GEERAQEIFA KYNKDKKVRV FTFSVGQHNY DRGP IQWMA CENKGYYYEI PSIGAIRINT QEYLDVLGRP MVLAGDKAKQ VQWTNVYLDA LELGLVITGT LPVFNITGQF ENKTN LKNQ LILGVMGVDV SLEDIKRLTP RFTLCPNGYY FAIDPNGYVL LHPNLQPKPI GVGIPTINLR KRRPNVQNPK SQEPVT LDF LDAELENDIK VEIRNKMIDG ESGEKTFRTL VKSQDERYID KGNRTYTWTP VNGTDYSLAL VLPTYSFYYI KAKIEET IT QARYSETLKP DNFEESGYTF LAPRDYCSDL KPSDNNTEFL LNFNEFIDRK TPNNPSCNTD LINRVLLDAG FTNELVQN Y WSKQKNIKGV KARFVVTDGG ITRVYPKEAG ENWQENPETY EDSFYKRSLD NDNYVFTAPY FNKSGPGAYE SGIMVSKAV EIYIQGKLLK PAVVGIKIDV NSWIENFTKT SIRDPCAGPV CDCKRNSDVM DCVILDDGGF LLMANHDDYT NQIGRFFGEI DPSLMRHLV NISVYAFNKS YDYQSVCEPG AAPKQGAGHR SAYVPSIADI LQIGWWATAA AWSILQQFLL SLTFPRLLEA A DMEDDDFT ASMSKQSCIT EQTQYFFDND SKSFSGVLDC GNCSRIFHVE KLMNTNLIFI MVESKGTCPC DTRLLIQAEQ TS DGPDPCD MVKQPRYRKG PDVCFDNNVL EDYTDCGGVS GLNPSLWSII GIQFVLLWLV SGSRHCLL

UniProtKB: Voltage-dependent calcium channel subunit alpha-2/delta-1

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 5 / Number of copies: 9 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #6: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #7: methyl (4~{R})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]...

MacromoleculeName: methyl (4~{R})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyridine-3-carboxylate
type: ligand / ID: 7 / Number of copies: 1 / Formula: VFY
Molecular weightTheoretical: 357.304 Da
Chemical component information

ChemComp-VFY:
methyl (4~{R})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyridine-3-carboxylate

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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

Concentration5 mg/mL
BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 seconds before plunging.
DetailsrCav1.1-100R was in lipid nanodisc

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94695
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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