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- PDB-2vay: Calmodulin complexed with CaV1.1 IQ peptide -

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Basic information

Entry
Database: PDB / ID: 2vay
TitleCalmodulin complexed with CaV1.1 IQ peptide
Components
  • CALMODULIN
  • VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL SUBUNIT ALPHA-1S
KeywordsMETAL TRANSPORT / EXCITATION-CONTRACTION COUPLING / CAV / CALCIUM / TRANSPORT / ACETYLATION / METHYLATION / L-TYPE CALCIUM CHANNEL / DIHYDROPYRIDINE RECEPTOR / IONIC CHANNEL / ION TRANSPORT / TRANSMEMBRANE / PHOSPHORYLATION / ALPHA-1S SUBUNIT / CALCIUM TRANSPORT / UBL CONJUGATION / CALCIUM CHANNEL / SKELETAL MUSCLE / VOLTAGE-DEPENDENT / VOLTAGE-GATED CHANNEL
Function / homology
Function and homology information


skeletal muscle adaptation / extraocular skeletal muscle development / positive regulation of muscle contraction / high voltage-gated calcium channel activity / : / L-type voltage-gated calcium channel complex / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / myoblast fusion / endoplasmic reticulum organization ...skeletal muscle adaptation / extraocular skeletal muscle development / positive regulation of muscle contraction / high voltage-gated calcium channel activity / : / L-type voltage-gated calcium channel complex / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / myoblast fusion / endoplasmic reticulum organization / NCAM1 interactions / I band / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / voltage-gated calcium channel complex / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / neuromuscular junction development / response to corticosterone / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / cellular response to caffeine / negative regulation of peptidyl-threonine phosphorylation / calcium ion import across plasma membrane / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / small molecule binding / RHO GTPases activate PAKs / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / voltage-gated calcium channel activity / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / phosphatidylinositol 3-kinase binding / eNOS activation / skeletal muscle fiber development / enzyme regulator activity / striated muscle contraction / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / muscle contraction / Activation of AMPK downstream of NMDARs / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / release of sequestered calcium ion into cytosol / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / T-tubule / response to amphetamine / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization
Similarity search - Function
Voltage-dependent calcium channel, L-type, alpha-1S subunit / 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 / : / Voltage-dependent channel domain superfamily ...Voltage-dependent calcium channel, L-type, alpha-1S subunit / 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 / : / 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-3 / Voltage-dependent L-type calcium channel subunit alpha-1S
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsHalling, D.B. / Black, D.J. / Pedersen, S.E. / Hamilton, S.L.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Determinants in Cav1 Channels that Regulate the Ca2+ Sensitivity of Bound Calmodulin.
Authors: Halling, D.B. / Georgiou, D.K. / Black, D.J. / Yang, G. / Fallon, J.L. / Quiocho, F.A. / Pedersen, S.E. / Hamilton, S.L.
History
DepositionSep 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CALMODULIN
B: VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL SUBUNIT ALPHA-1S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5147
Polymers19,3182
Non-polymers1965
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-22.6 kcal/mol
Surface area10600 Å2
MethodPQS
Unit cell
Length a, b, c (Å)84.920, 34.670, 62.980
Angle α, β, γ (deg.)90.00, 113.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CALMODULIN / CAM


Mass: 16535.186 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET 3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL SUBUNIT ALPHA-1S / CAV1.1-IQ / VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT ALPHA CAV1.1


Mass: 2783.250 Da / Num. of mol.: 1 / Fragment: RESIDUES 1522-1542 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q13698
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 47.7 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.3
Details: HANGING DROP VAPOR DIFFUSION 1.5 UL 10 MG/ML COMPLEX IN 20 MM MOPS PH7.4, 150 MM NACL, 4 MM CACL2 MIX WITH 4.5 UL WELL SOLUTION, 32% PEG 3350, 50 MM TRIS PH 8.3, 50 MM MGCL2, 5 DAYS AT 20-22 DEGREES C

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38079
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38079 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 15915 / % possible obs: 89.9 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.1
Reflection shellResolution: 1.86→1.94 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.65 / % possible all: 74.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F3Y

2f3y


Resolution: 1.94→19.77 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 495044.77 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1211 10.1 %RANDOM
Rwork0.218 ---
obs0.218 12021 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.6907 Å2 / ksol: 0.321955 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.95 Å20 Å2-3.28 Å2
2--13.63 Å20 Å2
3----6.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.94→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1348 0 5 127 1480
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.771.5
X-RAY DIFFRACTIONc_mcangle_it2.82
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.322.5
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 199 11.1 %
Rwork0.272 1591 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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