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- PDB-3dvm: Crystal Structure of Ca2+/CaM-CaV2.1 IQ domain complex -

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Basic information

Entry
Database: PDB / ID: 3dvm
TitleCrystal Structure of Ca2+/CaM-CaV2.1 IQ domain complex
Components
  • Calmodulin
  • Voltage-dependent P/Q-type calcium channel subunit alpha-1A
KeywordsMEMBRANE PROTEIN / calmodulin / calcium channel / IQ domain / inactivation / facilitation / calcium-dependent / voltage-gated
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / high voltage-gated calcium channel activity / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / negative regulation of peptidyl-threonine phosphorylation / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / high voltage-gated calcium channel activity / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / negative regulation of peptidyl-threonine phosphorylation / 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 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of ryanodine-sensitive calcium-release channel activity / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / positive regulation of DNA binding / Loss of phosphorylation of MECP2 at T308 / voltage-gated calcium channel complex / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / response to corticosterone / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / negative regulation of ryanodine-sensitive calcium-release channel activity / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of protein autophosphorylation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / calcium ion import across plasma membrane / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / adenylate cyclase binding / Regulation of MECP2 expression and activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / voltage-gated calcium channel activity / calcium channel inhibitor activity / activation of adenylate cyclase activity / cellular response to interferon-beta / Protein methylation / presynaptic cytosol / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / positive regulation of nitric-oxide synthase activity / titin binding / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / voltage-gated potassium channel complex / regulation of calcium-mediated signaling / calcium channel complex / substantia nigra development / FCERI mediated Ca+2 mobilization / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / calyx of Held / nitric-oxide synthase regulator activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / regulation of cytokinesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, P/Q-type, alpha-1 A / 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 ...Voltage-dependent calcium channel, P/Q-type, alpha-1 A / 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 / Voltage-dependent P/Q-type calcium channel subunit alpha-1A / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,5676
Polymers19,4072
Non-polymers1604
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-81 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.956, 43.956, 337.870
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 P/Q-type calcium channel subunit alpha-1A / Voltage-gated calcium channel subunit alpha Cav2.1 / Calcium channel / L type / alpha-1 polypeptide ...Voltage-gated calcium channel subunit alpha Cav2.1 / Calcium channel / L type / alpha-1 polypeptide isoform 4 / Brain calcium channel I / BI


Mass: 2685.301 Da / Num. of mol.: 1 / Fragment: UNP residues 1963-1982
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CACNA1A, CACH4, CACN3, CACNL1A4 / Plasmid: pET28b-HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: P27884
#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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, 25 % PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
1,2,3,41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.11587
SYNCHROTRONALS 8.3.120.97957
SYNCHROTRONALS 8.3.130.97969
SYNCHROTRONALS 8.3.141.01987
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 22, 2008
ADSC QUANTUM 3152CCDFeb 22, 2008
ADSC QUANTUM 3153CCDFeb 22, 2008
ADSC QUANTUM 3154CCDFeb 22, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
3MADMx-ray1
4MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
20.979571
30.979691
41.019871
ReflectionResolution: 2.6→20 Å / Num. obs: 6481 / % possible obs: 94.7 % / Redundancy: 16.4 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.272 / Num. unique all: 456 / % possible all: 72.3

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97967.52-8.42
13 wavelength20.97974.54-10.31
13 wavelength31.01990.7-2.03
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.8650.2710.030.592
2Se600.0830.350.0280.692
3Se600.2930.8930.0340.584
4Se52.010.2720.80.0250.414
5Se600.1090.6010.0540.5
6Se600.920.4070.0310.538
7Se600.2290.7710.0530.486
Phasing MAD expt
ID
1
3 wavelength
Phasing dmFOM : 0.76 / FOM acentric: 0.76 / FOM centric: 0.77 / Reflection: 4807 / Reflection acentric: 3076 / Reflection centric: 1731
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.3-29.8660.960.980.9526071189
5.2-8.30.890.920.87713364349
4.1-5.20.890.920.85830507323
3.6-4.10.830.860.77792531261
3.1-3.60.70.710.661397990407
2.9-3.10.510.510.52815613202

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.869 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.722 / SU B: 31.09 / SU ML: 0.344 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.681 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32 310 4.8 %RANDOM
Rwork0.276 ---
obs0.278 6460 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.16 Å2 / Biso mean: 58.034 Å2 / Biso min: 20.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å21.14 Å20 Å2
2--2.28 Å20 Å2
3----3.42 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 4 10 1188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211187
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.951602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47926.66754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07915185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.112152
X-RAY DIFFRACTIONr_chiral_restr0.0810.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02907
X-RAY DIFFRACTIONr_mcbond_it2.4224796
X-RAY DIFFRACTIONr_mcangle_it3.88551242
X-RAY DIFFRACTIONr_scbond_it3.0284391
X-RAY DIFFRACTIONr_scangle_it4.3125360
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.478 20 -
Rwork0.376 297 -
all-317 -
obs--70.13 %
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)
15.399-2.68792.55416.84532.41098.4380.94380.93550.2327-1.0794-1.0091-0.40890.41370.73980.0653-0.10030.33270.13640.53630.2004-0.14191.818430.6776152.6869
25.8086-4.5247-0.7766.7866-0.33745.2631-0.00670.35110.15110.0464-0.42920.1635-0.4708-0.31290.4359-0.15850.0492-0.07810.32230.10540.009110.51249.7598163.4134
34.37756.07575.097319.5549.88426.64520.0289-0.1160.3556-0.8299-0.0991-0.62440.35450.4630.0702-0.27320.13060.08140.25390.0486-0.03119.914826.2796157.2018
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 7011 - 70
2X-RAY DIFFRACTION2AA83 - 14583 - 145
3X-RAY DIFFRACTION3BB1961 - 19821 - 22

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