[English] 日本語
Yorodumi
- PDB-3bxl: Crystal structure of the R-type calcium channeL (CaV2.3) IQ domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bxl
TitleCrystal structure of the R-type calcium channeL (CaV2.3) IQ domain and CA2+calmodulin complex
Components
  • Calmodulin
  • Voltage-dependent R-type calcium channel subunit alpha-1E peptide
KeywordsMEMBRANE PROTEIN / SIGNALING PROTEIN / ION CHANNEL / CALMODULIN / CALCIUM CHANNEL / IQ DOMAIN / FACILLITATION / INACTIVATION / CALCIUM-DEPENDENT / VOLTAGE-GATED / ROBETTA / SIMULATIONS / Acetylation / Methylation / Phosphoprotein / Ubl conjugation / Calcium transport / Glycoprotein / Ion transport / Ionic channel / Membrane / Transmembrane / Transport / Voltage-gated channel
Function / homology
Function and homology information


regulation of somatostatin secretion / low voltage-gated calcium channel activity / voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / regulation of store-operated calcium channel activity / Presynaptic depolarization and calcium channel opening / Regulation of insulin secretion / regulation of high voltage-gated calcium channel activity / : / Presynaptic depolarization and calcium channel opening / presynaptic endocytosis ...regulation of somatostatin secretion / low voltage-gated calcium channel activity / voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / regulation of store-operated calcium channel activity / Presynaptic depolarization and calcium channel opening / Regulation of insulin secretion / regulation of high voltage-gated calcium channel activity / : / Presynaptic depolarization and calcium channel opening / presynaptic endocytosis / flagellated sperm motility / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / high voltage-gated calcium channel activity / : / regulation of insulin secretion involved in cellular response to glucose stimulus / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / fear response / establishment of protein localization to membrane / nervous system process / voltage-gated monoatomic cation channel activity / presynaptic cytosol / calcium ion import / regulation of synaptic vesicle endocytosis / voltage-gated calcium channel complex / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / postsynaptic cytosol / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / regulation of cardiac muscle cell action potential / positive regulation of DNA binding / response to pain / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / calcium ion import across plasma membrane / transmission of nerve impulse / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / behavioral response to pain / : / adenylate cyclase binding / calyx of Held / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / behavioral fear response / voltage-gated calcium channel activity / calcium channel inhibitor activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / voltage-gated potassium channel complex / activation of adenylate cyclase activity / enzyme regulator activity / GABA-ergic synapse / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / : / titin binding / regulation of calcium-mediated signaling / sperm midpiece / sensory perception of pain / calcium channel complex / potassium ion transmembrane transport / nitric-oxide synthase regulator activity / adenylate cyclase activator activity / response to amphetamine / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / positive regulation of nitric-oxide synthase activity / regulation of cytokinesis / spindle microtubule / establishment of localization in cell / locomotory behavior / Regulation of insulin secretion / positive regulation of receptor signaling pathway via JAK-STAT / calcium-mediated signaling / calcium ion transmembrane transport / visual learning / Schaffer collateral - CA1 synapse / cellular response to type II interferon / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / disordered domain specific binding / calcium ion transport / myelin sheath / glucose homeostasis / presynaptic membrane / growth cone / chemical synaptic transmission / perikaryon
Similarity search - Function
Voltage-dependent calcium channel, R-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 / : / Voltage-dependent channel domain superfamily ...Voltage-dependent calcium channel, R-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 / : / Voltage-dependent channel domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-1 / Voltage-dependent R-type calcium channel subunit alpha-1E / Voltage-dependent R-type calcium channel subunit alpha-1E
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMori, M.X. / Vander Kooi, C.W. / Leahy, D.J. / Yue, D.T.
CitationJournal: To be Published
Title: Crystal structure of the CaV2 IQ domain in complex with Ca2+/calmodulin
Authors: Mori, M.X. / Vander Kooi, C.W. / Leahy, D.J. / Yue, D.T.
History
DepositionJan 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calmodulin
B: Voltage-dependent R-type calcium channel subunit alpha-1E peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7048
Polymers19,3522
Non-polymers3526
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
MethodPISA
2
A: Calmodulin
B: Voltage-dependent R-type calcium channel subunit alpha-1E peptide
hetero molecules

A: Calmodulin
B: Voltage-dependent R-type calcium channel subunit alpha-1E peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,40816
Polymers38,7034
Non-polymers70512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,-y-1/2,-z+1/41
Buried area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.606, 124.606, 74.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-153-

SO4

21A-170-

HOH

31A-199-

HOH

41A-221-

HOH

-
Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calm1, Calm, Cam, Cam1 / Plasmid: PET24B / Production host: Escherichia coli (E. coli) / References: UniProt: P62161, UniProt: P0DP29*PLUS
#2: Protein/peptide Voltage-dependent R-type calcium channel subunit alpha-1E peptide


Mass: 2630.242 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized (Genbank accession no. Q15878).
References: UniProt: Q07652, UniProt: Q15878*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.86 %

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 12496

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.242 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26162 642 4.9 %RANDOM
Rwork0.20493 ---
obs0.20768 12496 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.193 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 14 138 1443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221315
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.9711767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7775164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.40626.11172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44415249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.035157
X-RAY DIFFRACTIONr_chiral_restr0.0870.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02997
X-RAY DIFFRACTIONr_nbd_refined0.2050.2678
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2119
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.217
X-RAY DIFFRACTIONr_mcbond_it0.6221.5838
X-RAY DIFFRACTIONr_mcangle_it1.02121289
X-RAY DIFFRACTIONr_scbond_it1.1423537
X-RAY DIFFRACTIONr_scangle_it1.8744.5476
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 53 -
Rwork0.282 878 -
obs--98.21 %

+
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://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