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- EMDB-6475: Cryo-EM structure of the rabbit voltage-gated calcium channel Cav... -

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Basic information

Entry
Database: EMDB / ID: EMD-6475
TitleCryo-EM structure of the rabbit voltage-gated calcium channel Cav1.1 at 4.2 angstrom resolution
Map dataReconstruction of a membrane protein
Sample
  • Sample: a membrane protein cryo-sample
  • Protein or peptide: Voltage-dependent L-type calcium channel subunit alpha-1S
  • Protein or peptide: Voltage-dependent L-type calcium channel subunit beta-2
  • Protein or peptide: Voltage-dependent calcium channel gamma-1 subunit
  • Protein or peptide: Voltage-dependent calcium channel subunit alpha-2/delta-1
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / voltage-gated calcium channel activity involved in AV node cell action potential / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / Regulation of insulin secretion / Presynaptic depolarization and calcium channel opening / membrane depolarization during atrial cardiac muscle cell action potential / high voltage-gated calcium channel activity / photoreceptor ribbon synapse ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / voltage-gated calcium channel activity involved in AV node cell action potential / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / Regulation of insulin secretion / Presynaptic depolarization and calcium channel opening / membrane depolarization during atrial cardiac muscle cell action potential / high voltage-gated calcium channel activity / photoreceptor ribbon synapse / membrane depolarization during AV node cell action potential / L-type voltage-gated calcium channel complex / positive regulation of muscle contraction / positive regulation of calcium ion transport / calcium ion import / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / cellular response to caffeine / regulation of heart rate by cardiac conduction / calcium ion import across plasma membrane / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / visual perception / T-tubule / muscle contraction / protein localization to plasma membrane / calcium channel regulator activity / phosphoprotein binding / sarcolemma / calcium ion transmembrane transport / actin filament binding / calcium ion transport / presynapse / chemical synaptic transmission / transmembrane transporter binding / calmodulin binding / protein domain specific binding / protein kinase binding / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent calcium channel, gamma-1 subunit / Voltage-dependent calcium channel, L-type, alpha-1S subunit / PMP-22/EMP/MP20/Claudin tight junction / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term ...Voltage-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent calcium channel, gamma-1 subunit / Voltage-dependent calcium channel, L-type, alpha-1S subunit / PMP-22/EMP/MP20/Claudin tight junction / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage gated calcium channel subunit beta domain 4Aa N terminal / 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 / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / Voltage-dependent channel domain superfamily / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Ion transport domain / Ion transport protein / P-loop containing nucleoside triphosphate hydrolase
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 / Voltage-dependent L-type calcium channel subunit beta-2 / Voltage-dependent L-type calcium channel subunit beta-2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWu JP / Yan Z / Li ZQ / Yan N
CitationJournal: 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
DepositionSep 28, 2015-
Header (metadata) releaseDec 9, 2015-
Map releaseDec 30, 2015-
UpdateJan 13, 2016-
Current statusJan 13, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jbr
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6475.gif

Downloads & links

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Map

FileDownload / File: emd_6475.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of a membrane protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.07917605 - 0.15899228
Average (Standard dev.)-0.00014582 (±0.00476387)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.920337.920337.920
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-189
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0790.159-0.000

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Supplemental data

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Sample components

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Entire : a membrane protein cryo-sample

EntireName: a membrane protein cryo-sample
Components
  • Sample: a membrane protein cryo-sample
  • Protein or peptide: Voltage-dependent L-type calcium channel subunit alpha-1S
  • Protein or peptide: Voltage-dependent L-type calcium channel subunit beta-2
  • Protein or peptide: Voltage-dependent calcium channel gamma-1 subunit
  • Protein or peptide: Voltage-dependent calcium channel subunit alpha-2/delta-1

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Supramolecule #1000: a membrane protein cryo-sample

SupramoleculeName: a membrane protein cryo-sample / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 4
Molecular weightTheoretical: 450 KDa

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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 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: rabbit / Tissue: muscle
Molecular weightTheoretical: 210 KDa
SequenceUniProtKB: Voltage-dependent L-type calcium channel subunit alpha-1S

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Macromolecule #2: Voltage-dependent L-type calcium channel subunit beta-2

MacromoleculeName: Voltage-dependent L-type calcium channel subunit beta-2
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: rabbit / Tissue: muscle
Molecular weightTheoretical: 30 KDa
SequenceUniProtKB: Voltage-dependent L-type calcium channel subunit beta-2

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Macromolecule #3: Voltage-dependent calcium channel gamma-1 subunit

MacromoleculeName: Voltage-dependent calcium channel gamma-1 subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: rabbit / Tissue: muscle
Molecular weightTheoretical: 25 KDa
SequenceUniProtKB: Voltage-dependent calcium channel gamma-1 subunit

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Macromolecule #4: Voltage-dependent calcium channel subunit alpha-2/delta-1

MacromoleculeName: Voltage-dependent calcium channel subunit alpha-2/delta-1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: rabbit / Tissue: muscle
Molecular weightTheoretical: 125 KDa
SequenceUniProtKB: Voltage-dependent calcium channel subunit alpha-2/delta-1

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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

Concentration0.1 mg/mL
BufferpH: 7.4 / Details: 200mM NaCl, 20mM MOPS, 0.5mM CaCl2, 0.1% digitonin
GridDetails: carbon coated grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateFeb 2, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 3991 / Average electron dose: 50 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0033 µm / Nominal defocus min: 0.002 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using RELION.
CTF correctionDetails: each micrograph
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 353372

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Atomic model buiding 1

Initial modelPDB ID:

1t0j

SoftwareName: Chimera, Situs
DetailsThe fitting is mostly refer to a related entry
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-3jbr:
Cryo-EM structure of the rabbit voltage-gated calcium channel Cav1.1 complex at 4.2 angstrom

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