+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9515 | |||||||||
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Title | ClassII map of the rabbit voltage-gated calcium channel Cav1.1 | |||||||||
Map data | ClassII map | |||||||||
Sample |
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Keywords | complex / channel / membrane protein | |||||||||
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 / cellular response to caffeine / calcium ion import across plasma membrane / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / muscle contraction ...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 / cellular response to caffeine / calcium ion import across plasma membrane / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / muscle contraction / release of sequestered calcium ion into cytosol / T-tubule / calcium ion transmembrane transport / sarcolemma / transmembrane transporter binding / calmodulin binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Wu JP / Yan Z | |||||||||
Funding support | China, 2 items
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Citation | Journal: Nature / Year: 2016 Title: Structure of the voltage-gated calcium channel Ca(v)1.1 at 3.6 Å resolution. Authors: Jianping Wu / Zhen Yan / Zhangqiang Li / Xingyang Qian / Shan Lu / Mengqiu Dong / Qiang Zhou / Nieng Yan / Abstract: The voltage-gated calcium (Ca) channels convert membrane electrical signals to intracellular Ca-mediated events. Among the ten subtypes of Ca channel in mammals, Ca1.1 is specified for the excitation- ...The voltage-gated calcium (Ca) channels convert membrane electrical signals to intracellular Ca-mediated events. Among the ten subtypes of Ca channel in mammals, Ca1.1 is specified for the excitation-contraction coupling of skeletal muscles. Here we present the cryo-electron microscopy structure of the rabbit Ca1.1 complex at a nominal resolution of 3.6 Å. The inner gate of the ion-conducting α1-subunit is closed and all four voltage-sensing domains adopt an 'up' conformation, suggesting a potentially inactivated state. The extended extracellular loops of the pore domain, which are stabilized by multiple disulfide bonds, form a windowed dome above the selectivity filter. One side of the dome provides the docking site for the α2δ-1-subunit, while the other side may attract cations through its negative surface potential. The intracellular I-II and III-IV linker helices interact with the β-subunit and the carboxy-terminal domain of α1, respectively. Classification of the particles yielded two additional reconstructions that reveal pronounced displacement of β and adjacent elements in α1. The atomic model of the Ca1.1 complex establishes a foundation for mechanistic understanding of excitation-contraction coupling and provides a three-dimensional template for molecular interpretations of the functions and disease mechanisms of Ca and Na channels. | |||||||||
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_9515.map.gz | 28.4 MB | EMDB map data format | |
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Header (meta data) | emd-9515-v30.xml emd-9515.xml | 20.5 KB 20.5 KB | Display Display | EMDB header |
Images | emd_9515.png | 156 KB | ||
Filedesc metadata | emd-9515.cif.gz | 8.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9515 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9515 | HTTPS FTP |
-Validation report
Summary document | emd_9515_validation.pdf.gz | 506.6 KB | Display | EMDB validaton report |
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Full document | emd_9515_full_validation.pdf.gz | 506.1 KB | Display | |
Data in XML | emd_9515_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_9515_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9515 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9515 | HTTPS FTP |
-Related structure data
Related structure data | 5gjwMC 9513C 9514C 5gjvC C: citing same article (ref.) M: atomic model generated by this map |
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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_9515.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ClassII map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : voltage-gated calcium channel Cav1.1
Entire | Name: voltage-gated calcium channel Cav1.1 |
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Components |
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-Supramolecule #1: voltage-gated calcium channel Cav1.1
Supramolecule | Name: voltage-gated calcium channel Cav1.1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 Details: The protein complex was endogenous purified from rabbit muscle tissue. |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: Voltage-dependent L-type calcium channel subunit alpha-1S
Macromolecule | Name: Voltage-dependent L-type calcium channel subunit alpha-1S type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 212.240594 KDa |
Sequence | String: 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 |
-Macromolecule #2: Voltage-dependent L-type calcium channel subunit beta-1
Macromolecule | Name: Voltage-dependent L-type calcium channel subunit beta-1 type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 11.974729 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SLEVLFQGPH MALRKEAERQ ALAQLEKAKT KPVAFAVRTN VGYNPSPGDE VPVEGVAITF EPKDFLHIKE KYNNDWWIGR LVKEGCEVG FIPSPVKLDS LRLLQEQ UniProtKB: Voltage-dependent L-type calcium channel subunit beta-1 |
-Macromolecule #3: Voltage-dependent L-type calcium channel subunit beta-1
Macromolecule | Name: Voltage-dependent L-type calcium channel subunit beta-1 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 22.356846 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: VPPYDVVPSM RPIILVGPSL KGYEVTDMMQ KALFDFLKHL FDGRISITRV TADISLAKRS VLNNPSKHII IERSNTRSSL AEVQSEIER IFELARTLQL VALDADTINH PAQLSKTSLA PIIVYIKITS PKVLQRLIKS RGKSQSKHLN VQIAASEKLA Q CPPEMFDI ...String: VPPYDVVPSM RPIILVGPSL KGYEVTDMMQ KALFDFLKHL FDGRISITRV TADISLAKRS VLNNPSKHII IERSNTRSSL AEVQSEIER IFELARTLQL VALDADTINH PAQLSKTSLA PIIVYIKITS PKVLQRLIKS RGKSQSKHLN VQIAASEKLA Q CPPEMFDI ILDENQLEDA CEHLAEYLEA YWKATHPPSS T UniProtKB: Voltage-dependent L-type calcium channel subunit beta-1 |
-Macromolecule #4: Voltage-dependent calcium channel gamma-1 subunit
Macromolecule | Name: Voltage-dependent calcium channel gamma-1 subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 25.082254 KDa |
Sequence | String: 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 |
-Macromolecule #5: Voltage-dependent calcium channel subunit alpha-2/delta-1
Macromolecule | Name: Voltage-dependent calcium channel subunit alpha-2/delta-1 type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 125.156 KDa |
Sequence | String: 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 VNGTDYSSLA LVLPTYSFYY IKAKIEE TI TQARYSETLK PDNFEESGYT FLAPRDYCSD LKPSDNNTEF LLNFNEFIDR KTPNNPSCNT DLINRVLLDA GFTNELVQ N YWSKQKNIKG VKARFVVTDG GITRVYPKEA GENWQENPET YEDSFYKRSL DNDNYVFTAP YFNKSGPGAY ESGIMVSKA VEIYIQGKLL KPAVVGIKID VNSWIENFTK TSIRDPCAGP VCDCKRNSDV MDCVILDDGG FLLMANHDDY TNQIGRFFGE IDPSLMRHL VNISVYAFNK SYDYQSVCEP GAAPKQGAGH RSAYVPSIAD ILQIGWWATA AAWSILQQFL LSLTFPRLLE A ADMEDDDF TASMSKQSCI TEQTQYFFDN DSKSFSGVLD CGNCSRIFHV EKLMNTNLIF IMVESKGTCP CDTRLLIQAE QT SDGPDPC DMVKQPRYRK GPDVCFDNNV LEDYTDC(ETA)GV SGLNPSLWSI IGIQFVLLWL VSGSRHCLL UniProtKB: Voltage-dependent calcium channel subunit alpha-2/delta-1 |
-Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 8 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #10: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 10 / Number of copies: 3 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 Details: 100 mM Tris-HCl, pH 8.0,200 mM NaCl, 10 mM CaCl2,15 mM reduced glutathione, 0.1% digitonin, and protease inhibitors. |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV Details: Grids were blotted for 2 s and flash-frozen in liquid ethane cooled by liquid nitrogen. |
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 5 / Number real images: 9704 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 0.0029 µm / Calibrated defocus min: 0.0013000000000000002 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-5gjw: |