[English] 日本語
Yorodumi
- PDB-1t3l: Structural Analysis of the Voltage-Dependent Calcium Channel Beta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t3l
TitleStructural Analysis of the Voltage-Dependent Calcium Channel Beta Subunit Functional Core in Complex with Alpha1 Interaction Domain
Components
  • Dihydropyridine-sensitive L-type, calcium channel beta-2 subunit
  • Voltage-dependent L-type calcium channel alpha-1S subunit
KeywordsTRANSPORT PROTEIN / protein-peptide complex / SH3 domain / Guanylate Kinase domain
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / voltage-gated calcium channel activity involved in AV node cell action potential / membrane depolarization during atrial cardiac muscle cell action potential / positive regulation of muscle contraction / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / photoreceptor ribbon synapse / positive regulation of calcium ion transport / calcium ion import / cellular response to caffeine ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / voltage-gated calcium channel activity involved in AV node cell action potential / membrane depolarization during atrial cardiac muscle cell action potential / positive regulation of muscle contraction / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / photoreceptor ribbon synapse / positive regulation of calcium ion transport / calcium ion import / cellular response to caffeine / calcium ion import across plasma membrane / regulation of heart rate by cardiac conduction / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / muscle contraction / release of sequestered calcium ion into cytosol / T-tubule / visual perception / calcium ion transmembrane transport / actin filament binding / presynapse / chemical synaptic transmission / transmembrane transporter binding / calmodulin binding / metal ion binding / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent calcium channel, L-type, alpha-1S subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage-dependent calcium channel, L-type, beta subunit / 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 / : ...Voltage-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent calcium channel, L-type, alpha-1S subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage-dependent calcium channel, L-type, beta subunit / 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 / : / 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 / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SH3 Domains / Voltage-dependent channel domain superfamily / SH3 type barrels. / 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 nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Voltage-dependent L-type calcium channel subunit alpha-1S / Voltage-dependent L-type calcium channel subunit beta-2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOpatowsky, Y. / Chen, C.-C. / Campbell, K.P. / Hirsch, J.A.
Citation
Journal: NEURON / Year: 2004
Title: Structural Analysis of Voltage-Dependent Calcium Channel Beta Subunit Functional Core and Its Complex with the Alpha1 Interaction Domain
Authors: Opatowsky, Y. / Chen, C.-C. / Campbell, K.P. / Hirsch, J.A.
#1: Journal: To be published
Title: Expression, Purification and Crystallization of a Functional Core of the Voltage-Dependent Calcium Channel Beta Subunit
Authors: Opatowsky, Y. / Chomsky-Hecht, O. / Hirsch, J.A.
History
DepositionApr 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE THE SEQUENCE OF THE PROTEIN IS FROM SWISSPROT P54288, ISOFORM 2A. RESIDUES 138-141 IN THE ...SEQUENCE THE SEQUENCE OF THE PROTEIN IS FROM SWISSPROT P54288, ISOFORM 2A. RESIDUES 138-141 IN THE COORDINATES WERE INTRODUCED INTO THE PROTEIN. THEY REPLACE RESIDUES 138-202 FROM THE NATIVE SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydropyridine-sensitive L-type, calcium channel beta-2 subunit
B: Voltage-dependent L-type calcium channel alpha-1S subunit


Theoretical massNumber of molelcules
Total (without water)40,5252
Polymers40,5252
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-13 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.775, 168.262, 34.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Dihydropyridine-sensitive L-type, calcium channel beta-2 subunit / Voltage-Dependent Calcium Channel Beta-2 Subunit / CAB2


Mass: 38340.953 Da / Num. of mol.: 1 / Fragment: Functional Core (Residues 25-422) / Mutation: P122R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CACNB2, CACNLB2 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54288
#2: Protein/peptide Voltage-dependent L-type calcium channel alpha-1S subunit / Calcium channel / L type / alpha-1 polypeptide / isoform 3 / skeletal muscle


Mass: 2184.363 Da / Num. of mol.: 1 / Fragment: AID / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is from Oryctolagus cuniculus (rabbit) gene CACNA1S.
References: UniProt: P07293
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 20K, Bicine, sodium chloride, beta-mercaptoethanol, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0069 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0069 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 19123 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059 / Net I/σ(I): 21.3
Reflection shellHighest resolution: 2.2 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.9 / % possible all: 63.2

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→84.52 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.447 / SU ML: 0.186 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28201 1283 6.9 %RANDOM
Rwork0.22138 ---
obs0.22554 17364 83.77 %-
all-18647 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.992 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å20 Å20 Å2
2--3.7 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→84.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 0 128 2671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212594
X-RAY DIFFRACTIONr_bond_other_d0.0030.022390
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9553513
X-RAY DIFFRACTIONr_angle_other_deg0.85835568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022859
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02500
X-RAY DIFFRACTIONr_nbd_refined0.2220.2657
X-RAY DIFFRACTIONr_nbd_other0.2520.22884
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.21607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3160.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4850.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.011.51621
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91822618
X-RAY DIFFRACTIONr_scbond_it2.5543973
X-RAY DIFFRACTIONr_scangle_it4.2534.5895
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 60
Rwork0.258 858

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more