[English] 日本語
Yorodumi
- PDB-3dvk: Crystal Structure of Ca2+/CaM-CaV2.3 IQ domain complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dvk
TitleCrystal Structure of Ca2+/CaM-CaV2.3 IQ domain complex
Components
  • Calmodulin
  • Voltage-dependent R-type calcium channel subunit alpha-1E
KeywordsMEMBRANE PROTEIN / calmodulin / calcium channel / IQ domain / inactivation / facilitation / calcium-dependent / voltage-gated
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 / Presynaptic depolarization and calcium channel opening / Regulation of insulin secretion / flagellated sperm motility / : / regulation of insulin secretion involved in cellular response to glucose stimulus / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding ...regulation of somatostatin secretion / low voltage-gated calcium channel activity / voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / Presynaptic depolarization and calcium channel opening / Regulation of insulin secretion / flagellated sperm motility / : / regulation of insulin secretion involved in cellular response to glucose stimulus / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / high voltage-gated calcium channel activity / fear response / voltage-gated monoatomic cation channel activity / calcium ion import / nervous system process / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / regulation of synaptic vesicle endocytosis / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / Activation of RAC1 downstream of NMDARs / response to pain / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / autophagosome membrane docking / response to corticosterone / voltage-gated calcium channel complex / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / transmission of nerve impulse / negative regulation of peptidyl-threonine phosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / behavioral response to pain / Synthesis of IP3 and IP4 in the cytosol / nitric-oxide synthase binding / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / calcium ion import across plasma membrane / Uptake and function of anthrax toxins / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / GABA-ergic synapse / Smooth Muscle Contraction / voltage-gated calcium channel activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / behavioral fear response / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of protein autophosphorylation / sensory perception of pain / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity
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 / EF-hand / Recoverin; domain 1 ...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 / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-3 / Voltage-dependent R-type calcium channel subunit alpha-1E
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKim, E.Y. / Rumpf, C.H. / Fujiwara, Y. / Cooley, E.S. / Van Petegem, F. / Minor, D.L.
CitationJournal: Structure / Year: 2008
Title: Structures of Ca(V)2 Ca(2+)/CaM-IQ Domain Complexes Reveal Binding Modes that Underlie Calcium-Dependent Inactivation and Facilitation.
Authors: Kim, E.Y. / Rumpf, C.H. / Fujiwara, Y. / Cooley, E.S. / Van Petegem, F. / Minor, D.L.
History
DepositionJul 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6106
Polymers19,4502
Non-polymers1604
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-76 kcal/mol
Surface area9090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.262, 44.262, 337.941
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-512-

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.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Plasmid: pEGST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Voltage-dependent R-type calcium channel subunit alpha-1E / Voltage-gated calcium channel subunit alpha Cav2.3 / Calcium channel / L type / alpha-1 polypeptide ...Voltage-gated calcium channel subunit alpha Cav2.3 / Calcium channel / L type / alpha-1 polypeptide / isoform 6 / Brain calcium channel II / RBE-II / RBE2 / BII


Mass: 2728.366 Da / Num. of mol.: 1 / Fragment: UNP residues 1818-1837
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cacna1e, Cach6, Cacnl1a6 / Plasmid: pET28b-HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: Q07652
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, 25-30 % PEG 2000 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2007
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 9377 / % possible obs: 95.2 % / Redundancy: 15.9 % / Rmerge(I) obs: 0.103
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.383 / Num. unique all: 631 / % possible all: 68.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.6 Å
Translation2.5 Å19.6 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.783 / SU B: 14.388 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.359 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 439 4.7 %RANDOM
Rwork0.256 ---
obs0.258 9294 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 105.09 Å2 / Biso mean: 71.425 Å2 / Biso min: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å21.14 Å20 Å2
2--2.29 Å20 Å2
3----3.43 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1245 0 4 34 1283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211266
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9521699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4555163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79825.53865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24715215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.384157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02975
X-RAY DIFFRACTIONr_mcbond_it2.3274812
X-RAY DIFFRACTIONr_mcangle_it3.50151279
X-RAY DIFFRACTIONr_scbond_it2.8944454
X-RAY DIFFRACTIONr_scangle_it3.9285420
LS refinement shellResolution: 2.3→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 21 -
Rwork0.267 408 -
all-429 -
obs--63.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.93741.3824-0.77064.43890.32493.23480.2485-0.0506-0.0630.5511-0.5211-0.2378-0.37861.14320.2726-0.2937-0.2961-0.10950.33620.2503-0.2147-19.15359.126317.21
23.01312.14890.41225.3877-1.39423.97520.1557-0.053-0.05020.0554-0.20830.26210.2786-0.08160.0527-0.3641-0.00020.0417-0.0290.0858-0.173-11.106727.88055.9724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 77
2X-RAY DIFFRACTION2A79 - 147

+
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