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- PDB-3dve: Crystal Structure of Ca2+/CaM-CaV2.2 IQ domain complex -

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Basic information

Entry
Database: PDB / ID: 3dve
TitleCrystal Structure of Ca2+/CaM-CaV2.2 IQ domain 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


: / 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 ...: / 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 / regulation of synaptic vesicle endocytosis / 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) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / 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 / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / 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 / Long-term potentiation / Ion transport by P-type ATPases / 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 / Smooth Muscle Contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of DNA binding / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / 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 / protein serine/threonine kinase activator activity / nitric-oxide synthase regulator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / mitochondrial membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / Stimuli-sensing channels / synaptic vesicle membrane / spindle pole
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 / EF-hand / Recoverin; domain 1 ...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. / Ion transport domain / Ion transport protein / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / 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: 2.35 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)19,7107
Polymers19,4912
Non-polymers2195
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-85 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.303, 40.303, 344.652
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: 2769.225 Da / Num. of mol.: 1 / Fragment: UNP residues 1855-1875
Source method: isolated from a genetically manipulated source
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: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
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: Nov 3, 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: 2.35→20 Å / Num. obs: 7844 / % possible obs: 99.3 % / Redundancy: 15 % / Rmerge(I) obs: 0.134 / Χ2: 0.646 / Net I/σ(I): 3.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.425 / Num. unique all: 700 / Χ2: 0.358 / % possible all: 97

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å20.02 Å
Translation2.5 Å20.02 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: 2.35→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.808 / SU B: 13.012 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.419 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 358 4.6 %RANDOM
Rwork0.207 ---
obs0.21 7757 99.35 %-
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: 81.58 Å2 / Biso mean: 30.339 Å2 / Biso min: 8.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å20 Å2
2---0.54 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 5 78 1337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221308
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.961764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5445171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03725.91571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97215239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.382157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021007
X-RAY DIFFRACTIONr_mcbond_it0.7461.5814
X-RAY DIFFRACTIONr_mcangle_it1.48221300
X-RAY DIFFRACTIONr_scbond_it2.4553494
X-RAY DIFFRACTIONr_scangle_it4.1764.5458
LS refinement shellResolution: 2.35→2.413 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 26 -
Rwork0.204 483 -
all-509 -
obs--93.05 %
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)
10.38890.7706-0.16031.7307-1.36895.48580.02570.0292-0.01410.05940.0574-0.18170.3461-0.0803-0.08310.01860.0086-0.0125-0.00550.01850.0019-1.719620.641717.341
20.52890.1978-0.21420.2334-0.91374.44540.0728-0.06710.11950.1980.09810.1884-0.2667-0.2962-0.1709-0.00330.02830.0490.03770.0163-0.0067-8.086730.079920.6052
34.7570.57650.09392.7359-0.95762.5546-0.1330.17030.4022-0.00660.03110.0091-0.1615-0.01570.1019-0.02230.0023-0.0084-0.06060.00380.0109-11.074213.08182.6398
43.06190.86540.81520.7985-0.87852.9551-0.0224-0.11320.03160.1962-0.0598-0.0653-0.0692-0.06290.08230.00060.0134-0.0129-0.02630.0007-0.0077-14.03535.20789.4638
50.854-1.93780.95179.6907-2.35081.12670.04550.05710.08840.0072-0.0618-0.03550.0564-0.00380.0163-0.0515-0.00370.0123-0.0023-0.0001-0.001-11.988323.650311.7206
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 - 18751 - 23

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