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Open data
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Basic information
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Title | Cryo-EM structure of human Cav3.2 with ACT-709478 | |||||||||
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![]() | Cav3.2 / voltage gated calcium channel / cryo-EM / TRANSPORT PROTEIN / ACT-709478 | |||||||||
Function / homology | ![]() low voltage-gated calcium channel activity / aldosterone biosynthetic process / cortisol biosynthetic process / positive regulation of acrosome reaction / high voltage-gated calcium channel activity / cellular response to potassium ion / voltage-gated monoatomic ion channel activity / myoblast fusion / NCAM1 interactions / calcium ion import ...low voltage-gated calcium channel activity / aldosterone biosynthetic process / cortisol biosynthetic process / positive regulation of acrosome reaction / high voltage-gated calcium channel activity / cellular response to potassium ion / voltage-gated monoatomic ion channel activity / myoblast fusion / NCAM1 interactions / calcium ion import / inorganic cation transmembrane transport / muscle organ development / voltage-gated calcium channel complex / regulation of heart contraction / calcium ion import across plasma membrane / Smooth Muscle Contraction / muscle contraction / cellular response to hormone stimulus / regulation of membrane potential / scaffold protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Fan X / Huang J / Yan N | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for human Ca3.2 inhibition by selective antagonists. Authors: Jian Huang / Xiao Fan / Xueqin Jin / Chen Lyu / Qinmeng Guo / Tao Liu / Jiaofeng Chen / Amaël Davakan / Philippe Lory / Nieng Yan / ![]() ![]() ![]() Abstract: The Ca3.2 subtype of T-type calcium channels has been targeted for developing analgesics and anti-epileptics for its role in pain and epilepsy. Here we present the cryo-EM structures of Ca3.2 alone ...The Ca3.2 subtype of T-type calcium channels has been targeted for developing analgesics and anti-epileptics for its role in pain and epilepsy. Here we present the cryo-EM structures of Ca3.2 alone and in complex with four T-type calcium channel selective antagonists with overall resolutions ranging from 2.8 Å to 3.2 Å. The four compounds display two binding poses. ACT-709478 and TTA-A2 both place their cyclopropylphenyl-containing ends in the central cavity to directly obstruct ion flow, meanwhile extending their polar tails into the IV-I fenestration. TTA-P2 and ML218 project their 3,5-dichlorobenzamide groups into the II-III fenestration and place their hydrophobic tails in the cavity to impede ion permeation. The fenestration-penetrating mode immediately affords an explanation for the state-dependent activities of these antagonists. Structure-guided mutational analysis identifies several key residues that determine the T-type preference of these drugs. The structures also suggest the role of an endogenous lipid in stabilizing drug binding in the central cavity. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.4 KB 17.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 40.2 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() | 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9aylMC ![]() 9aygC ![]() 9ayhC ![]() 9ayjC ![]() 9aykC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.036 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_43995_half_map_1.map | ||||||||||||
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-Half map: #2
File | emd_43995_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Voltage-dependent T-type calcium channel subunit alpha-1H
Entire | Name: Voltage-dependent T-type calcium channel subunit alpha-1H |
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Components |
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-Supramolecule #1: Voltage-dependent T-type calcium channel subunit alpha-1H
Supramolecule | Name: Voltage-dependent T-type calcium channel subunit alpha-1H type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Voltage-dependent T-type calcium channel subunit alpha-1H
Macromolecule | Name: Voltage-dependent T-type calcium channel subunit alpha-1H type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 234.853609 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMTEGARA ADEVRVPLGA PPPGPAALVG ASPESPGAPG REAERGSEL GVSPSESPAA ERGAELGADE EQRVPYPALA ATVFFCLGQT TRPRSWCLRL VCNPWFEHVS MLVIMLNCVT L GMFRPCED ...String: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMTEGARA ADEVRVPLGA PPPGPAALVG ASPESPGAPG REAERGSEL GVSPSESPAA ERGAELGADE EQRVPYPALA ATVFFCLGQT TRPRSWCLRL VCNPWFEHVS MLVIMLNCVT L GMFRPCED VECGSERCNI LEAFDAFIFA FFAVEMVIKM VALGLFGQKC YLGDTWNRLD FFIVVAGMME YSLDGHNVSL SA IRTVRVL RPLRAINRVP SMRILVTLLL DTLPMLGNVL LLCFFVFFIF GIVGVQLWAG LLRNRCFLDS AFVRNNNLTF LRP YYQTEE GEENPFICSS RRDNGMQKCS HIPGRRELRM PCTLGWEAYT QPQAEGVGAA RNACINWNQY YNVCRSGDSN PHNG AINFD NIGYAWIAIF QVITLEGWVD IMYYVMDAHS FYNFIYFILL IIVGSFFMIN LCLVVIATQF SETKQRESQL MREQR ARHL SNDSTLASFS EPGSCYEELL KYVGHIFRKV KRRSLRLYAR WQSRWRKKVD PGWMGRLWVT FSGKLRRIVD SKYFSR GIM MAILVNTLSM GVEYHEQPEE LTNALEISNI VFTSMFALEM LLKLLACGPL GYIRNPYNIF DGIIVVISVW EIVGQAD GG LSVLRTFRLL RVLKLVRFLP ALRRQLVVLV KTMDNVATFC TLLMLFIFIF SILGMHLFGC KFSLKTDTGD TVPDRKNF D SLLWAIVTVF QILTQEDWNV VLYNGMASTS SWAALYFVAL MTFGNYVLFN LLVAILVEGF QAEGDANRSD TDEDKTSVH FEEDFHKLRE LQTTELKMCS LAVTPNGHLE GRGSLSPPLI MCTAATPMPT PKSSPFLDAA PSLPDSRRGS SSSGDPPLGD QKPPASLRS SPCAPWGPSG AWSSRRSSWS SLGRAPSLKR RGQCGERESL LSGEGKGSTD DEAEDGRAAP GPRATPLRRA E SLDPRPLR PAALPPTKCR DRDGQVVALP SDFFLRIDSH REDAAELDDD SEDSCCLRLH KVLEPYKPQW CRSREAWALY LF SPQNRFR VSCQKVITHK MFDHVVLVFI FLNCVTIALE RPDIDPGSTE RVFLSVSNYI FTAIFVAEMM VKVVALGLLS GEH AYLQSS WNLLDGLLVL VSLVDIVVAM ASAGGAKILG VLRVLRLLRT LRPLRVISRA PGLKLVVETL ISSLRPIGNI VLIC CAFFI IFGILGVQLF KGKFYYCEGP DTRNISTKAQ CRAAHYRWVR RKYNFDNLGQ ALMSLFVLSS KDGWVNIMYD GLDAV GVDQ QPVQNHNPWM LLYFISFLLI VSFFVLNMFV GVVVENFHKC RQHQEAEEAR RREEKRLRRL ERRRRSTFPS PEAQRR PYY ADYSPTRRSI HSLCTSHYLD LFITFIICVN VITMSMEHYN QPKSLDEALK YCNYVFTIVF VFEAALKLVA FGFRRFF KD RWNQLDLAIV LLSLMGITLE EIEMSAALPI NPTIIRIMRV LRIARVLKLL KMATGMRALL DTVVQALPQV GNLGLLFM L LFFIYAALGV ELFGRLECSE DNPCEGLSRH ATFSNFGMAF LTLFRVSTGD NWNGIMKDTL RECSREDKHC LSYLPALSP VYFVTFVLVA QFVLVNVVVA VLMKHLEESN KEAREDAELD AEIELEMAQG PGSARRVDAD RPPLPQESPG ARDAPNLVAR KVSVSRMLS LPNDSYMFRP VVPASAPHPR PLQEVEMETY GAGTPLGSVA SVHSPPAESC ASLQIPLAVS SPARSGEPLH A LSPRGTAR SPSLSRLLCR QEAVHTDSLE GKIDSPRDTL DPAEPGEKTP VRPVTQGGSL QSPPRSPRPA SVRTRKHTFG QR CVSSRPA APGGEEAEAS DPADEEVSHI TSSACPWQPT AEPHGPEASP VAGGERDLRR LYSVDAQGFL DKPGRADEQW RPS AELGSG EPGEAKAWGP EAEPALGARR KKKMSPPCIS VEPPAEDEGS ARPSAAEGGS TTLRRRTPSC EATPHRDSLE PTEG SGAGG DPAAKGERWG QASCRAEHLT VPSFAFEPLD LGVPSGDPFL DGSHSVTPES RASSSGAIVP LEPPESEPPM PVGDP PEKR RGLYLTVPQC PLEKPGSPSA TPAPGGGADD PV UniProtKB: Voltage-dependent T-type calcium channel subunit alpha-1H, Voltage-dependent T-type calcium channel subunit alpha-1H |
-Macromolecule #2: N-{1-[(5-cyanopyridin-2-yl)methyl]-1H-pyrazol-3-yl}-2-{4-[1-(trif...
Macromolecule | Name: N-{1-[(5-cyanopyridin-2-yl)methyl]-1H-pyrazol-3-yl}-2-{4-[1-(trifluoromethyl)cyclopropyl]phenyl}acetamide type: ligand / ID: 2 / Number of copies: 1 / Formula: A1AHK |
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Molecular weight | Theoretical: 425.406 Da |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #5: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: LPE |
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Molecular weight | Theoretical: 510.708 Da |
Chemical component information | ![]() ChemComp-LPE: |
-Macromolecule #6: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 4 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ![]() ChemComp-Y01: |
-Macromolecule #7: [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoy...
Macromolecule | Name: [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate type: ligand / ID: 7 / Number of copies: 4 / Formula: JL3 |
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Molecular weight | Theoretical: 663.906 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |