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- PDB-3dvj: Crystal Structure of Ca2+/CaM-CaV2.2 IQ domain (without cloning a... -

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Basic information

Entry
Database: PDB / ID: 3dvj
TitleCrystal Structure of Ca2+/CaM-CaV2.2 IQ domain (without cloning artifact, HM to TV) complex
Components
  • Calmodulin
  • Voltage-dependent N-type calcium channel subunit alpha-1B
KeywordsMEMBRANE PROTEIN / calmodulin / calcium channel / IQ domain / inactivation / facilitation / calcium-dependent / voltage-gated
Function / homology
Function and homology information


high voltage-gated calcium channel activity / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers ...high voltage-gated calcium channel activity / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / 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) / nitric-oxide synthase binding / response to corticosterone / positive regulation of DNA binding / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / regulation of synaptic vesicle exocytosis / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / negative regulation of peptidyl-threonine phosphorylation / calcineurin-mediated signaling / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of ryanodine-sensitive calcium-release channel activity / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of synaptic vesicle endocytosis / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / calcium ion import across plasma membrane / protein phosphatase activator activity / adenylate cyclase binding / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / regulation of cardiac muscle contraction / detection of calcium ion / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / voltage-gated calcium channel activity / presynaptic cytosol / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / activation of adenylate cyclase activity / positive regulation of protein autophosphorylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / eNOS activation / enzyme regulator activity / regulation of calcium-mediated signaling / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / substantia nigra development / positive regulation of peptidyl-threonine phosphorylation / calyx of Held / nitric-oxide synthase regulator activity / response to amphetamine / FCERI mediated Ca+2 mobilization / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / regulation of heart rate / sarcomere / positive regulation of nitric-oxide synthase activity / protein serine/threonine kinase activator activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / regulation of cytokinesis / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of protein serine/threonine kinase activity / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT
Similarity search - Function
Voltage-dependent calcium channel, N-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, N-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 N-type calcium channel subunit alpha-1B
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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 / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,3096
Polymers19,1492
Non-polymers1604
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-58 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.321, 40.321, 348.558
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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 N-type calcium channel subunit alpha-1B / Voltage-gated calcium channel subunit alpha Cav2.2 / Calcium channel / L type / alpha-1 polypeptide ...Voltage-gated calcium channel subunit alpha Cav2.2 / Calcium channel / L type / alpha-1 polypeptide isoform 5 / Brain calcium channel III / BIII


Mass: 2427.835 Da / Num. of mol.: 1 / Fragment: UNP residues 1853-1873
Source method: isolated from a genetically manipulated source
Details: cloning artifact residues (HM) were mutated to original channel sequence(TV)
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CACNA1B, CACH5, CACNL1A5 / Plasmid: pET28b-HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: Q05152
#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


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
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

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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: Jan 18, 2008
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: 2.8→20 Å / Num. obs: 4823 / % possible obs: 98.1 % / Redundancy: 11 % / Rmerge(I) obs: 0.133 / Χ2: 0.708 / Net I/σ(I): 4.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.443 / Num. unique all: 479 / Χ2: 0.356 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.5 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å19.86 Å
Translation2.8 Å19.86 Å

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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: 2.8→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.748 / SU B: 31.147 / SU ML: 0.33 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.298 219 4.6 %RANDOM
Rwork0.248 ---
obs0.25 4746 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.49 Å2 / Biso mean: 45.518 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0.43 Å20 Å2
2---0.86 Å20 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 4 10 1218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221225
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9481655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4235160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.80825.90261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87815197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.207155
X-RAY DIFFRACTIONr_chiral_restr0.080.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02941
X-RAY DIFFRACTIONr_mcbond_it1.9884795
X-RAY DIFFRACTIONr_mcangle_it3.35651259
X-RAY DIFFRACTIONr_scbond_it2.474430
X-RAY DIFFRACTIONr_scangle_it3.8275395
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 19 -
Rwork0.27 328 -
all-347 -
obs--99.71 %
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)
10.2184-0.2887-1.33451.06180.94449.14230.091-0.056-0.25240.0512-0.04050.1088-0.56340.4305-0.05050.0988-0.0515-0.01030.1413-0.0059-0.019-17.861513.865617.1063
21.57230.7142-2.63150.86240.36888.95180.1797-0.4762-0.38280.2313-0.0238-0.05370.3911.316-0.156-0.10650.0516-0.04870.24580.0025-0.0419-11.74565.081520.6193
32.76820.2192-1.47685.50192.34934.608-0.27530.113-0.32580.17150.1398-0.08810.40580.06170.13550.0868-0.0210.0185-0.07920.02620.0675-8.142921.91272.6273
45.8734-1.1447-1.43052.71161.71212.7523-0.0886-0.24990.07660.15790.02740.07340.2864-0.0330.06130.08340.00740.0069-0.0193-0.0092-0.0097-5.434629.80889.3874
52.3821-3.7243-2.48612.60232.82842.75980.1068-0.1247-0.0014-0.02350.04340.1386-0.20570.3483-0.1502-0.086-0.0078-0.02420.0223-0.04880.006-7.4912.287612.1881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 395 - 39
2X-RAY DIFFRACTION2AA45 - 7545 - 75
3X-RAY DIFFRACTION3AA82 - 11282 - 112
4X-RAY DIFFRACTION4AA118 - 146118 - 146
5X-RAY DIFFRACTION5BB1853 - 18731 - 21

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