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- PDB-3bxk: Crystal structure of the P/Q-type calcium channel (CaV2.1) IQ dom... -

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Basic information

Entry
Database: PDB / ID: 3bxk
TitleCrystal structure of the P/Q-type calcium channel (CaV2.1) IQ domain and CA2+calmodulin complex
Components
  • Calmodulin
  • Voltage-dependent P/Q-type calcium channel subunit alpha-1A peptide
KeywordsMEMBRANE PROTEIN / SIGNALING PROTEIN / ION CHANNEL / CALMODULIN / CALCIUM CHANNEL / IQ DOMAIN / FACILLITATION / INACTIVATION / CALCIUM-DEPENDENT / VOLTAGE-GATED / ROBETTA / SIMULATIONS / Acetylation / Methylation / Phosphoprotein / Calcium transport / Glycoprotein / Ion transport / Ionic channel / Membrane / Transmembrane / Transport / Voltage-gated channel
Function / homology
Function and homology information


regulation of store-operated calcium channel activity / : / : / Presynaptic depolarization and calcium channel opening / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / high voltage-gated calcium channel activity / : / : ...regulation of store-operated calcium channel activity / : / : / Presynaptic depolarization and calcium channel opening / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / high voltage-gated calcium channel activity / : / : / : / : / : / transporter inhibitor activity / : / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / syntaxin binding / positive regulation of DNA binding / voltage-gated calcium channel complex / negative regulation of high voltage-gated calcium channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / response to corticosterone / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle cell action potential / presynaptic endocytosis / response to amyloid-beta / calcineurin-mediated signaling / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / adenylate cyclase binding / calcium ion import across plasma membrane / protein phosphatase activator activity / regulation of synaptic vesicle endocytosis / detection of calcium ion / postsynaptic cytosol / cell surface receptor signaling pathway via JAK-STAT / regulation of cardiac muscle contraction / voltage-gated calcium channel activity / catalytic complex / phosphatidylinositol 3-kinase binding / activation of adenylate cyclase activity / enzyme regulator activity / positive regulation of nitric-oxide synthase activity / calcium channel inhibitor activity / presynaptic cytosol / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cell projection / titin binding / regulation of calcium-mediated signaling / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / regulation of heart rate / calyx of Held / nitric-oxide synthase regulator activity / adenylate cyclase activator activity / sarcomere / response to amphetamine / regulation of cytokinesis / protein serine/threonine kinase activator activity / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / calcium channel regulator activity / Regulation of insulin secretion / calcium-mediated signaling / response to calcium ion / cellular response to type II interferon / modulation of chemical synaptic transmission / G2/M transition of mitotic cell cycle / calcium ion transmembrane transport / Schaffer collateral - CA1 synapse / cellular response to amyloid-beta / spindle pole / disordered domain specific binding / calcium-dependent protein binding / protein autophosphorylation / myelin sheath / synaptic vesicle membrane / amyloid-beta binding / growth cone / positive regulation of cytosolic calcium ion concentration / sperm midpiece / vesicle / transmembrane transporter binding / neuron projection / positive regulation of apoptotic process / protein domain specific binding / neuronal cell body / calcium ion binding / centrosome / protein kinase binding / chromatin
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
Voltage-dependent P/Q-type calcium channel subunit alpha-1A / Calmodulin-1 / Calmodulin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMori, M.X. / Vander Kooi, C.W. / Leahy, D.J. / Yue, D.T.
CitationJournal: To be Published
Title: Crystal structure of the P/Q-type calcium channel (CaV2.1) IQ domain and CA2+calmodulin complex
Authors: Mori, M.X. / Vander Kooi, C.W. / Leahy, D.J. / Yue, D.T.
History
DepositionJan 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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 peptide
C: Calmodulin
D: Voltage-dependent P/Q-type calcium channel subunit alpha-1A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,25215
Polymers38,6434
Non-polymers60911
Water95553
1
A: Calmodulin
B: Voltage-dependent P/Q-type calcium channel subunit alpha-1A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5787
Polymers19,3222
Non-polymers2565
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
MethodPISA
2
C: Calmodulin
D: Voltage-dependent P/Q-type calcium channel subunit alpha-1A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6748
Polymers19,3222
Non-polymers3526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.655, 80.431, 63.837
Angle α, β, γ (deg.)90.00, 97.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calm1, Calm, Cam, Cam1 / Plasmid: PET24B / Production host: Escherichia coli (E. coli) / References: UniProt: P62161, UniProt: P0DP29*PLUS
#2: Protein/peptide Voltage-dependent P/Q-type calcium channel subunit alpha-1A peptide


Mass: 2600.193 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. This sequence occurs naturally in humans
References: UniProt: O00555
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.69 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorDate: Oct 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 13241

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→24.87 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / SU B: 11.546 / SU ML: 0.251 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.655 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26703 635 4.9 %RANDOM
Rwork0.21291 ---
obs0.2157 12283 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.931 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20.23 Å2
2--0.1 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.55→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 23 53 2584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222565
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.9713436
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2745313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16725.915142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.79115492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.091515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021939
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.21193
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21762
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.150.228
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.215
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0220.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7671.51615
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34322497
X-RAY DIFFRACTIONr_scbond_it1.54831056
X-RAY DIFFRACTIONr_scangle_it2.5624.5938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 45 -
Rwork0.275 833 -
obs--94 %
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)
14.7534-1.061-1.06643.276-1.756622.85290.0679-0.3238-0.33840.18220.2170.18860.9813-0.0071-0.2848-0.08910.1364-0.0157-0.27560.0143-0.1714-25.044-38.184-6.808
23.05052.1843-0.30892.19051.397125.00170.1774-0.2880.23670.05820.2009-0.5726-0.8522.5179-0.3783-0.06850.0918-0.01980.1294-0.0211-0.177-16.324-32.84-7.85
39.3523-2.89092.29726.8712-3.137310.6523-0.0507-0.1783-0.32230.27250.0282-0.40010.0370.49560.0225-0.08780.02240.0532-0.19470.0566-0.0569-30.753-22.728-20.391
49.4127-3.98851.82099.2189-2.80623.63680.2216-0.5344-1.5720.22590.09610.97280.5504-0.574-0.3177-0.08490.0350.10770.07620.2249-0.0398-40.152-25.996-17.36
547.497414.58943.705311.57610.064710.1090.8097-2.174-0.71960.7040.10920.94380.2739-1.0363-0.9189-0.03170.1449-0.0215-0.2510.2769-0.181-33.235-32.437-9.344
66.18820.424.7795.4222-1.376119.2644-0.1644-0.00520.51810.3273-0.137-0.4788-0.17710.4270.3014-0.0688-0.04360.0141-0.3337-0.1194-0.144-19.4977.054-17.698
74.34642.10384.63853.37661.303215.9281-0.015-0.82450.02160.2762-0.04540.6722-0.0947-2.11250.0604-0.0604-0.00240.02090.1011-0.0774-0.1772-29.4356.358-14.212
83.40982.6559-0.28219.1286-2.819112.42130.01180.03190.03150.2895-0.10280.2286-0.9932-0.05770.091-0.1126-0.07970.0464-0.1279-0.0557-0.0989-28.343-7.499-30.101
98.00285.2949-1.45410.749-0.10513.50610.15670.1149-0.70160.305-0.1086-1.3295-0.26450.8302-0.0481-0.1996-0.0858-0.02750.029-0.0162-0.1222-18.222-9.773-30.83
1043.7141-6.4349-16.218815.74139.007716.04820.1274-0.32530.13590.4419-0.0382-0.916-0.30760.5494-0.0891-0.0197-0.1754-0.1705-0.3266-0.0007-0.3029-18.76-1.295-22.324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 394 - 39
2X-RAY DIFFRACTION2AA40 - 7540 - 75
3X-RAY DIFFRACTION3AA81 - 10681 - 106
4X-RAY DIFFRACTION4AA107 - 145107 - 145
5X-RAY DIFFRACTION5BB1960 - 19761 - 17
6X-RAY DIFFRACTION6CC4 - 394 - 39
7X-RAY DIFFRACTION7CC40 - 8040 - 80
8X-RAY DIFFRACTION8CC81 - 10681 - 106
9X-RAY DIFFRACTION9CC107 - 146107 - 146
10X-RAY DIFFRACTION10DD1960 - 19781 - 19

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