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Yorodumi- PDB-6byo: Residue assignment correction to the voltage gated calcium Cav1.1... -
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-Basic information
Entry | Database: PDB / ID: 6byo | |||||||||
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Title | Residue assignment correction to the voltage gated calcium Cav1.1 rabbit alpha 1 subunit PDB entries 3JBR & 5GJV | |||||||||
Components | Voltage-dependent L-type calcium channel subunit alpha-1S | |||||||||
Keywords | MEMBRANE PROTEIN / Voltage-Gated Calcium Channels | |||||||||
Function / homology | Function and homology information positive regulation of muscle contraction / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / calcium ion import across plasma membrane / cellular response to caffeine / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / muscle contraction / release of sequestered calcium ion into cytosol / T-tubule ...positive regulation of muscle contraction / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / calcium ion import across plasma membrane / cellular response to caffeine / 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 / transmembrane transporter binding / calmodulin binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Cardozo, T.J. / Martinez-Ortiz, W. | |||||||||
Funding support | United States, 2items
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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. #1: Journal: Science / Year: 2015 Title: Structure of the voltage-gated calcium channel Cav1.1 complex. Authors: Jianping Wu / Zhen Yan / Zhangqiang Li / Chuangye Yan / Shan Lu / Mengqiu Dong / Nieng Yan / Abstract: The voltage-gated calcium channel Ca(v)1.1 is engaged in the excitation-contraction coupling of skeletal muscles. The Ca(v)1.1 complex consists of the pore-forming subunit α1 and auxiliary subunits ...The voltage-gated calcium channel Ca(v)1.1 is engaged in the excitation-contraction coupling of skeletal muscles. The Ca(v)1.1 complex consists of the pore-forming subunit α1 and auxiliary subunits α2δ, β, and γ. We report the structure of the rabbit Ca(v)1.1 complex determined by single-particle cryo-electron microscopy. The four homologous repeats of the α1 subunit are arranged clockwise in the extracellular view. The γ subunit, whose structure resembles claudins, interacts with the voltage-sensing domain of repeat IV (VSD(IV)), whereas the cytosolic β subunit is located adjacent to VSD(II) of α1. The α2 subunit interacts with the extracellular loops of repeats I to III through its VWA and Cache1 domains. The structure reveals the architecture of a prototypical eukaryotic Ca(v) channel and provides a framework for understanding the function and disease mechanisms of Ca(v) and Na(v) channels. | |||||||||
History |
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Remark 0 | THIS ENTRY 6BYO REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-9513, DETERMINED BY J.P.Wu,Z.Yan |
-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6byo.cif.gz | 438.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6byo.ent.gz | 358.1 KB | Display | PDB format |
PDBx/mmJSON format | 6byo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6byo_validation.pdf.gz | 852.2 KB | Display | wwPDB validaton report |
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Full document | 6byo_full_validation.pdf.gz | 871.7 KB | Display | |
Data in XML | 6byo_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 6byo_validation.cif.gz | 55.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/6byo ftp://data.pdbj.org/pub/pdb/validation_reports/by/6byo | HTTPS FTP |
-Related structure data
Related structure data | 9513M M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 155063.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P07293 |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Rabbit Voltage Gated Calcium Cav1.1 alpha 1 subunit. / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: PHENIX / Category: model fitting |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 3.6 Å / Resolution method: OTHER / Num. of particles: 527833 / Details: overall resolution of entire complex / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT |