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- PDB-3jbr: Cryo-EM structure of the rabbit voltage-gated calcium channel Cav... -

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Basic information

Entry
Database: PDB / ID: 3jbr
TitleCryo-EM structure of the rabbit voltage-gated calcium channel Cav1.1 complex at 4.2 angstrom
Components
  • (Voltage-dependent L-type calcium channel subunit ...) x 2
  • (Voltage-dependent calcium channel ...) x 2
KeywordsMEMBRANE PROTEIN / voltage-gated calcium channel
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 / 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 ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / 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
von Willebrand factor type A domain / 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 ...von Willebrand factor type A domain / 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 / 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
beta-D-mannopyranose / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWu, J.P. / Yan, Z. / 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 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references
Category: database_2 / em_image_scans ...database_2 / em_image_scans / em_software / struct_ref_seq_dif
Item: _em_software.fitting_id / _em_software.image_processing_id ..._em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _struct_ref_seq_dif.details
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Movie
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Voltage-dependent L-type calcium channel subunit alpha-1S
B: Voltage-dependent L-type calcium channel subunit beta-2
E: Voltage-dependent calcium channel gamma-1 subunit
F: Voltage-dependent calcium channel subunit alpha-2/delta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,53222
Polymers390,8144
Non-polymers3,71918
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Voltage-dependent L-type calcium channel subunit ... , 2 types, 2 molecules AB

#1: Protein Voltage-dependent L-type calcium channel subunit alpha-1S / Calcium channel / L type / alpha-1 polypeptide / isoform 3 / skeletal muscle / Voltage-gated ...Calcium channel / L type / alpha-1 polypeptide / isoform 3 / skeletal muscle / Voltage-gated calcium channel subunit alpha Cav1.1


Mass: 208655.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P07293
#2: Protein Voltage-dependent L-type calcium channel subunit beta-2 / CAB2 / Calcium channel voltage-dependent subunit beta 2'


Mass: 40300.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chain B is for a subunit that is docked by a homolog crystal structure (PDB code: 1T0J)
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VGC3

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Voltage-dependent calcium channel ... , 2 types, 2 molecules EF

#3: Protein Voltage-dependent calcium channel gamma-1 subunit / Dihydropyridine-sensitive L-type / skeletal muscle calcium channel subunit gamma


Mass: 25082.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P19518
#4: Protein Voltage-dependent calcium channel subunit alpha-2/delta-1 / Voltage-gated calcium channel subunit alpha-2/delta-1 / Voltage-dependent calcium channel subunit ...Voltage-gated calcium channel subunit alpha-2/delta-1 / Voltage-dependent calcium channel subunit alpha-2-1 / Voltage-dependent calcium channel subunit delta-1


Mass: 116775.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P13806

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Sugars , 2 types, 17 molecules

#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 1 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Details

Has protein modificationY
Sequence detailsRESIDUES 1396-1520 OF ENTITY 1 (CHAIN A), AND RESIDUES 40-55/662-955 OF ENTITY 4 (CHAIN F) ARE ...RESIDUES 1396-1520 OF ENTITY 1 (CHAIN A), AND RESIDUES 40-55/662-955 OF ENTITY 4 (CHAIN F) ARE MODELED AS UNK SINCE THE EM DENSITY IS NOT GOOD ENOUGH TO ASSIGN EXACTLY. THE REAL SEQUENCE OF RESIDUES 1396-1520 OF ENTITY 1 (CHAIN A) SHOULD BE (PHHLDEFKAIWAEYDPEAKGRIKHLDVVTLLRRIQPPLGFGKFCPHRVACKRLVGMNMPLNSDGTVTFNATLFALVRTALKIKTEGNFEQANEELRAIIKKIWKRTSMKLLDQVIPPIGDDEVTV). REAL SEQUENCES FOR RESIDUES 40-55/662-955 OF ENTITY 4 SHOULD BE (DMQEDLVTLAKTASG) AND (TFLAPRDYCSDLKPSDNNTEFLLNFNEFIDRKTPNNPSCNTDLINRVLLDAGFTNELVQNYWSKQKNIKGVKARFVVTDGGITRVYPKEAGENWQENPETYEDSFYKRSLDNDNYVFTAPYFNKSGPGAYESGIMVSKAVEIYIQGKLLKPAVVGIKIDVNSWIENFTKTSIRDPCAGPVCDCKRNSDVMDCVILDDGGFLLMANHDDYTNQIGRFFGEIDPSLMRHLVNISVYAFNKSYDYQSVCEPGAAPKQGAGHRSAYVPSIADILQIGWWATAAAWSILQQFLLSLTFP) RESPECTIVELY.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: a membrane protein cryo-sample / Type: COMPLEX / Synonym: Cav1.1
Molecular weightValue: 0.45 MDa / Experimental value: NO
Buffer solutionName: 20mM MOPS, 200mM NaCl, 0.5mM CaCl2,0.1% digitonin / pH: 7.4 / Details: 20mM MOPS, 200mM NaCl, 0.5mM CaCl2,0.1% digitonin
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: carbon coated grid
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 2 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Feb 2, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3.3 nm / Nominal defocus min: 2 nm / Cs: 2.7 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)

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Processing

EM software
IDNameCategory
1Situsmodel fitting
2UCSF Chimeramodel fitting
3RELION3D reconstruction
CTF correctionDetails: each micrograph
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 353372
Details: (Single particle details: The particles were selected using RELION.) (Single particle--Applied symmetry: C1)
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: REFINEMENT PROTOCOL--rigid body DETAILS--The fitting is mostly refer to a related entry
Atomic model buildingPDB-ID: 1T0J

1t0j


Accession code: 1T0J / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms16234 0 233 0 16467

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