[English] 日本語
Yorodumi
- PDB-1vyt: beta3 subunit complexed with aid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vyt
Titlebeta3 subunit complexed with aid
Components
  • CALCIUM CHANNEL BETA-3 SUBUNIT
  • VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT
KeywordsTRANSPORT PROTEIN / ION TRANSPORT-COMPLEX / CALCIUM CHANNEL BETA SUBUNIT / AID DOAMIN / ION TRANSPORT / IONIC CHANNEL / VOLTAGE-GATED CHANNEL / SH3 DOMAIN
Function / homology
Function and homology information


cell communication involved in cardiac conduction / negative regulation of detection of mechanical stimulus involved in sensory perception of touch / caveolar macromolecular signaling complex / : / regulation of membrane hyperpolarization / : / growth hormone secretion / Phase 2 - plateau phase / Phase 0 - rapid depolarisation / Presynaptic depolarization and calcium channel opening ...cell communication involved in cardiac conduction / negative regulation of detection of mechanical stimulus involved in sensory perception of touch / caveolar macromolecular signaling complex / : / regulation of membrane hyperpolarization / : / growth hormone secretion / Phase 2 - plateau phase / Phase 0 - rapid depolarisation / Presynaptic depolarization and calcium channel opening / voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / Regulation of insulin secretion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / immune system development / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane repolarization during action potential / positive regulation of high voltage-gated calcium channel activity / membrane depolarization during atrial cardiac muscle cell action potential / calcium ion transmembrane transport via high voltage-gated calcium channel / membrane depolarization during AV node cell action potential / positive regulation of adenylate cyclase activity / high voltage-gated calcium channel activity / cardiac conduction / L-type voltage-gated calcium channel complex / calcium-ion regulated exocytosis / smooth muscle contraction involved in micturition / membrane depolarization during cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell action potential / regulation of organ growth / cardiac muscle cell action potential involved in contraction / camera-type eye development / calcium ion import / embryonic forelimb morphogenesis / adult walking behavior / insulin secretion / calcium ion transport into cytosol / voltage-gated calcium channel complex / neuromuscular junction development / alpha-actinin binding / regulation of heart rate by cardiac conduction / plasma membrane => GO:0005886 / positive regulation of excitatory postsynaptic potential / calcium channel regulator activity / smooth muscle contraction / calcium ion import across plasma membrane / regulation of vasoconstriction / voltage-gated calcium channel activity / positive regulation of protein targeting to membrane / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / detection of mechanical stimulus involved in sensory perception of pain / translation initiation factor binding / T-tubule / protein phosphatase 2A binding / dendritic shaft / protein localization to plasma membrane / calcium ion transmembrane transport / postsynaptic density membrane / visual learning / sarcolemma / regulation of blood pressure / Z disc / intracellular calcium ion homeostasis / cellular response to amyloid-beta / calcium ion transport / glucose homeostasis / presynaptic membrane / heart development / T cell receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / cellular response to hypoxia / chemical synaptic transmission / postsynaptic membrane / perikaryon / transmembrane transporter binding / membrane => GO:0016020 / postsynaptic density / calmodulin binding / apical plasma membrane / protein domain specific binding / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein kinase binding / enzyme binding / cell surface / protein-containing complex / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Voltage-dependent calcium channel, L-type, beta-3 subunit / Voltage-dependent L-type calcium channel subunit beta-3, SH3 domain / Voltage-dependent calcium channel, L-type, alpha-1C 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-dependent calcium channel, L-type, beta-3 subunit / Voltage-dependent L-type calcium channel subunit beta-3, SH3 domain / Voltage-dependent calcium channel, L-type, alpha-1C 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. / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Voltage-dependent L-type calcium channel subunit alpha-1C / Voltage-dependent L-type calcium channel subunit beta-3
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, Y.-H. / Li, M.-H. / Zhang, Y. / He, L.-L. / Yamada, Y. / Fitzmaurice, A. / Yang, S. / Zhang, H. / Tong, L. / Yang, J.
CitationJournal: Nature / Year: 2004
Title: Structural Basis of the Alpha(1)-Beta Subunit Interaction of Voltage-Gated Ca(2+) Channels
Authors: Chen, Y.-H. / Li, M.-H. / Zhang, Y. / He, L.-L. / Yamada, Y. / Fitzmaurice, A. / Shen, Y. / Zhang, H. / Tong, L. / Yang, J.
History
DepositionMay 7, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CALCIUM CHANNEL BETA-3 SUBUNIT
B: CALCIUM CHANNEL BETA-3 SUBUNIT
E: VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT
F: VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT


Theoretical massNumber of molelcules
Total (without water)85,1534
Polymers85,1534
Non-polymers00
Water1,38777
1
A: CALCIUM CHANNEL BETA-3 SUBUNIT
E: VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT


Theoretical massNumber of molelcules
Total (without water)42,5762
Polymers42,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CALCIUM CHANNEL BETA-3 SUBUNIT
F: VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT


Theoretical massNumber of molelcules
Total (without water)42,5762
Polymers42,5762
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)252.300, 69.000, 60.700
Angle α, β, γ (deg.)90.00, 96.70, 90.00
Int Tables number5
Space group name H-MC121
DetailsAN INTERMOLECULAR DISULFIDE LINKAGE (A71CYS - B71CYS) ISLIKELY FORMED IN THE CRYSTAL PACKING DURING THECRYSTALLIZATION EXPERIMENT

-
Components

#1: Protein CALCIUM CHANNEL BETA-3 SUBUNIT / CAB3 / VOLTAGE-DEPENDENT CALCIUM CHANNEL BETA-3 SUBUNIT


Mass: 39494.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54287
#2: Protein/peptide VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT / CALCIUM CHANNEL L TYPE ALPHA-1 POLYPEPTIDE ISOFORM 1 FROM CARDIAC MUSCLE / RAT BRAIN CLASS C


Mass: 3081.388 Da / Num. of mol.: 2 / Fragment: RESIDUES 452-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22002
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE BETA SUBUNIT OF VOLTAGE-DEPENDENT CALCIUM CHANNELS CONTRIBUTES TO THE FUNCTION OF THE CALCIUM ...THE BETA SUBUNIT OF VOLTAGE-DEPENDENT CALCIUM CHANNELS CONTRIBUTES TO THE FUNCTION OF THE CALCIUM CHANNEL BY INCREASING PEAK CALCIUM CURRENT, SHIFTING THE VOLTAGE DEPENDENCIES OF ACTIVATION AND INACTIVATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 44 %
Crystal growpH: 8 / Details: TRIS-HCL PH 8.0, 150 MM MGCL2, 15 PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9202
DetectorDate: Mar 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 32147 / % possible obs: 96 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.319 / % possible all: 77

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
GCOMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VYU

1vyu


Resolution: 2.6→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.272 --
Rwork0.231 --
obs0.231 32147 96 %
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4885 0 0 77 4962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 10 / % reflection obs: 77 %

+
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