+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0792 | ||||||||||||||||||
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Title | calcium channel-ligand | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Function / homology | Function and homology information SA node cell to atrial cardiac muscle cell signaling / AV node cell to bundle of His cell signaling / sinoatrial node development / voltage-gated calcium channel activity involved SA node cell action potential / low voltage-gated calcium channel activity / voltage-gated calcium channel activity involved in AV node cell action potential / AV node cell action potential / SA node cell action potential / membrane depolarization during SA node cell action potential / response to nickel cation ...SA node cell to atrial cardiac muscle cell signaling / AV node cell to bundle of His cell signaling / sinoatrial node development / voltage-gated calcium channel activity involved SA node cell action potential / low voltage-gated calcium channel activity / voltage-gated calcium channel activity involved in AV node cell action potential / AV node cell action potential / SA node cell action potential / membrane depolarization during SA node cell action potential / response to nickel cation / membrane depolarization during AV node cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / high voltage-gated calcium channel activity / cardiac muscle cell action potential involved in contraction / NCAM1 interactions / calcium ion import / voltage-gated calcium channel complex / calcium ion import across plasma membrane / regulation of heart rate by cardiac conduction / Smooth Muscle Contraction / regulation of membrane potential / calcium ion transmembrane transport / scaffold protein binding / chemical synaptic transmission / synapse / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Yan N | ||||||||||||||||||
Funding support | China, 5 items
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Citation | Journal: Nature / Year: 2019 Title: Cryo-EM structures of apo and antagonist-bound human Ca3.1. Authors: Yanyu Zhao / Gaoxingyu Huang / Qiurong Wu / Kun Wu / Ruiqi Li / Jianlin Lei / Xiaojing Pan / Nieng Yan / Abstract: Among the ten subtypes of mammalian voltage-gated calcium (Ca) channels, Ca3.1-Ca3.3 constitute the T-type, or the low-voltage-activated, subfamily, the abnormal activities of which are associated ...Among the ten subtypes of mammalian voltage-gated calcium (Ca) channels, Ca3.1-Ca3.3 constitute the T-type, or the low-voltage-activated, subfamily, the abnormal activities of which are associated with epilepsy, psychiatric disorders and pain. Here we report the cryo-electron microscopy structures of human Ca3.1 alone and in complex with a highly Ca3-selective blocker, Z944, at resolutions of 3.3 Å and 3.1 Å, respectively. The arch-shaped Z944 molecule reclines in the central cavity of the pore domain, with the wide end inserting into the fenestration on the interface between repeats II and III, and the narrow end hanging above the intracellular gate like a plug. The structures provide the framework for comparative investigation of the distinct channel properties of different Ca subfamilies. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0792.map.gz | 116.6 MB | EMDB map data format | |
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Header (meta data) | emd-0792-v30.xml emd-0792.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_0792.png | 175.1 KB | ||
Masks | emd_0792_msk_1.map | 125 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0792 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0792 | HTTPS FTP |
-Validation report
Summary document | emd_0792_validation.pdf.gz | 520.9 KB | Display | EMDB validaton report |
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Full document | emd_0792_full_validation.pdf.gz | 520.4 KB | Display | |
Data in XML | emd_0792_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_0792_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0792 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0792 | HTTPS FTP |
-Related structure data
Related structure data | 6kzpMC 0791C 6kzoC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0792.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_0792_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : membrane protein-ligand
Entire | Name: membrane protein-ligand |
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Components |
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-Supramolecule #1: membrane protein-ligand
Supramolecule | Name: membrane protein-ligand / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Voltage-dependent T-type calcium channel subunit alpha-1G,Voltage...
Macromolecule | Name: Voltage-dependent T-type calcium channel subunit alpha-1G,Voltage-dependent T-type calcium channel subunit alpha-1G type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 238.874984 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MHHHHHHHHG DYKDDDDKGT DEEEDGAGAE ESGQPRSFMR LNDLSGAGGR PGPGSAEKDP GSADSEAEGL PYPALAPVVF FYLSQDSRP RSWCLRTVCN PWFERISMLV ILLNCVTLGM FRPCEDIACD SQRCRILQAF DDFIFAFFAV EMVVKMVALG I FGKKCYLG ...String: MHHHHHHHHG DYKDDDDKGT DEEEDGAGAE ESGQPRSFMR LNDLSGAGGR PGPGSAEKDP GSADSEAEGL PYPALAPVVF FYLSQDSRP RSWCLRTVCN PWFERISMLV ILLNCVTLGM FRPCEDIACD SQRCRILQAF DDFIFAFFAV EMVVKMVALG I FGKKCYLG DTWNRLDFFI VIAGMLEYSL DLQNVSFSAV RTVRVLRPLR AINRVPSMRI LVTLLLDTLP MLGNVLLLCF FV FFIFGIV GVQLWAGLLR NRCFLPENFS LPLSVDLERY YQTENEDESP FICSQPRENG MRSCRSVPTL RGDGGGGPPC GLD YEAYNS SSNTTCVNWN QYYTNCSAGE HNPFKGAINF DNIGYAWIAI FQVITLEGWV DIMYFVMDAH SFYNFIYFIL LIIV GSFFM INLCLVVIAT QFSETKQRES QLMREQRVRF LSNASTLASF SEPGSCYEEL LKYLVYILRK AARRLAQVSR AAGVR VGLL SSPAPLGGQE TQPSSSCSRS HRRLSVHHLV HHHHHHHHHY HLGACQSSCK ISSPCLKADS GACGPDSCPY CARAGA GEV ELADREMPDS DSEAVYEFTQ DAQHSDLRDP HSRRQRSLGP DAEPSSVLAF WRLICDTFRK IVDSKYFGRG IMIAILV NT LSMGIEYHEQ PEELTNALEI SNIVFTSLFA LEMLLKLLVY GPFGYIKNPY NIFDGVIVVI SVWEIVGQQG GGLSVLRT F RLMRVLKLVR FLPALQRQLV VLMKTMDNVA TFCMLLMLFI FIFSILGMHL FGCKFASERD GDTLPDRKNF DSLLWAIVT VFQILTQEDW NKVLYNGMAS TSSWAALYFI ALMTFGNYVL FNLLVAILVE GFQAEGDANK SESEPDFFSP SLDGDGDRKK CLALVSLGE HPELRKSLLP PLIIHTAATP MSLPKSTSTG LGEALGPASR RTSSSGSAEP GAAHEMKSPP SARSSPHSPW S AASSWTSR RSSRNSLGRA PSLKRRSPSG ERRSLLSGEG QESQDEEESS EEERASPAGS DHRHRGSLER EAKSSFDLPD TL QVPGLHR TASGRGSASE HQDCNGKSAS GRLARALRPD DPPLDGDDAD DEGNLSKGER VRAWIRARLP ACCLERDSWS AYI FPPQSR FRLLCHRIIT HKMFDHVVLV IIFLNCITIA MERPKIDPHS AERIFLTLSN YIFTAVFLAE MTVKVVALGW CFGE QAYLR SSWNVLDGLL VLISVIDILV SMVSDSGTKI LGMLRVLRLL RTLRPLRVIS RAQGLKLVVE TLMSSLKPIG NIVVI CCAF FIIFGILGVQ LFKGKFFVCQ GEDTRNITNK SDCAEASYRW VRHKYNFDNL GQALMSLFVL ASKDGWVDIM YDGLDA VGV DQQPIMNHNP WMLLYFISFL LIVAFFVLNM FVGVVVENFH KCRQHQEEEE ARRREEKRLR RLEKKRRNLM LDDVIAS GS SASAASEAQC KPYYSDYSRF RLLVHHLCTS HYLDLFITGV IGLNVVTMAM EHYQQPQILD EALKICNYIF TVIFVLES V FKLVAFGFRR FFQDRWNQLD LAIVLLSIMG ITLEEIEVNA SLPINPTIIR IMRVLRIARV LKLLKMAVGM RALLDTVMQ ALPQVGNLGL LFMLLFFIFA ALGVELFGDL ECDETHPCEG LGRHATFRNF GMAFLTLFRV STGDNWNGIM KDTLRDCDQE STCYNTVIS PIYFVSFVLT AQFVLVNVVI AVLMKHLEES NKEAKEEAEL EAELELEMKT LSPQPHSPLG SPFLWPGVEG P DSPDSPKP GALHPAAHAR SASHFSLEHP TMQPHPTELP GPDLLTVRKS GVSRTHSLPN DSYMCRHGST AEGPLGHRGW GL PKAQSGS VLSVHSQPAD TSYILQLPKD APHLLQPHSA PTWGTIPKLP PPGRSPLAQR PLRRQAAIRT DSLDVQGLGS RED LLAEVS GPSPPLARAY SFWGQSSTQA QQHSRSHSKI SKHMTPPAPC PGPEPNWGKG PPETRSSLEL DTELSWISGD LLPP GGQEE PPSPRDLKKC YSVEAQSCQR RPTSWLDEQR RHSIAVSCLD SGSQPHLGTD PSNLGGQPLG GPGSRPKKKL SPPSI TIDP PESQGPRTPP SPGICLRRRA PSSDSKDPLA SGPPDSMAAS PSPKKDVLSL SGLSSDPADL DP |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 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: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #4: ~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-...
Macromolecule | Name: ~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-4-yl]methyl]-3-chloranyl-5-fluoranyl-benzamide type: ligand / ID: 4 / Number of copies: 1 / Formula: DZR |
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Molecular weight | Theoretical: 383.888 Da |
Chemical component information | ChemComp-DZR: |
-Macromolecule #5: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
Macromolecule | Name: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / type: ligand / ID: 5 / Number of copies: 8 / Formula: 3PE |
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Molecular weight | Theoretical: 748.065 Da |
-Macromolecule #6: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 3 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138449 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |