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- PDB-6u3a: 1.65 Angstrom crystal structure of the N97S Ca-CaM:CaV1.2 IQ doma... -

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Basic information

Entry
Database: PDB / ID: 6u3a
Title1.65 Angstrom crystal structure of the N97S Ca-CaM:CaV1.2 IQ domain complex
Components
  • Calmodulin-1
  • Voltage-dependent L-type calcium channel subunit alpha-1C
KeywordsCALCIUM-BINDING PROTEIN/MEMBRANE PROTEIN / MEMBRANE PROTEIN / CALCIUM-BINDING PROTEIN-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / immune system development / positive regulation of adenylate cyclase activity / membrane depolarization during atrial cardiac muscle cell action potential / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of muscle contraction / membrane depolarization during AV node cell action potential / high voltage-gated calcium channel activity ...voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / immune system development / positive regulation of adenylate cyclase activity / membrane depolarization during atrial cardiac muscle cell action potential / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of muscle contraction / membrane depolarization during AV node cell action potential / high voltage-gated calcium channel activity / cardiac conduction / L-type voltage-gated calcium channel complex / membrane depolarization during cardiac muscle cell action potential / cell communication by electrical coupling involved in cardiac conduction / regulation of ventricular cardiac muscle cell action potential / camera-type eye development / NCAM1 interactions / cardiac muscle cell action potential involved in contraction / embryonic forelimb morphogenesis / calcium ion transport into cytosol / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / voltage-gated calcium channel complex / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / alpha-actinin binding / calcineurin-mediated signaling / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / calcium ion import across plasma membrane / Long-term potentiation / protein phosphatase activator activity / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / voltage-gated calcium channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / regulation of calcium-mediated signaling / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / Regulation of insulin secretion
Similarity search - Function
Voltage-dependent calcium channel, L-type, alpha-1C subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / 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 calcium channel, L-type, alpha-1C subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / 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 / : / 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 L-type calcium channel subunit alpha-1C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWang, K. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J. Physiol. (Lond.) / Year: 2020
Title: Arrhythmia mutations in calmodulin can disrupt cooperativity of Ca2+binding and cause misfolding.
Authors: Wang, K. / Brohus, M. / Holt, C. / Overgaard, M.T. / Wimmer, R. / Van Petegem, F.
History
DepositionAug 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,35313
Polymers42,0274
Non-polymers3279
Water5,423301
1
A: Calmodulin-1
C: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1807
Polymers21,0132
Non-polymers1665
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-84 kcal/mol
Surface area9210 Å2
MethodPISA
2
B: Calmodulin-1
D: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1746
Polymers21,0132
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-73 kcal/mol
Surface area8910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.419, 68.077, 86.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calmodulin-1


Mass: 16694.324 Da / Num. of mol.: 2 / Mutation: N97S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#2: Protein/peptide Voltage-dependent L-type calcium channel subunit alpha-1C / Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle / Voltage-gated calcium ...Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle / Voltage-gated calcium channel subunit alpha Cav1.2


Mass: 4318.968 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CACNA1C, CACH2, CACN2, CACNL1A1, CCHL1A1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13936
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: DL-malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 85584 / % possible obs: 98.6 % / Redundancy: 2.93 % / Biso Wilson estimate: 22.62 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.65-1.75138350.8131
4.93-35.66131730.9991

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BE6

2be6


Resolution: 1.65→35.661 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.16 / Phase error: 20.81
RfactorNum. reflection% reflection
Rfree0.2088 4283 5.01 %
Rwork0.178 --
obs0.1795 85568 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.12 Å2 / Biso mean: 32.6073 Å2 / Biso min: 12.13 Å2
Refinement stepCycle: final / Resolution: 1.65→35.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 9 301 2950
Biso mean--24.61 36.52 -
Num. residues----343
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6501-1.66880.29981450.2767269497
1.6688-1.68840.26511440.2643266699
1.6884-1.7090.26681390.2626270899
1.709-1.73070.32551450.266275399
1.7307-1.75340.32181420.2579270999
1.7534-1.77750.31651390.2476265899
1.7775-1.80290.28961470.2409278199
1.8029-1.82980.22151420.2262269899
1.8298-1.85840.24171460.215272599
1.8584-1.88880.2351440.2026267098
1.8888-1.92140.24681470.1965276599
1.9214-1.95630.22651400.1904266599
1.9563-1.99390.2111420.1942273099
1.9939-2.03460.19021430.1919269799
2.0346-2.07890.23171450.1934273999
2.0789-2.12720.23331370.1737273399
2.1272-2.18040.22171460.1736273399
2.1804-2.23940.19471390.1711269799
2.2394-2.30520.22981450.1634271599
2.3052-2.37960.17711440.168269598
2.3796-2.46470.23241440.1832270199
2.4647-2.56330.18921380.1738271799
2.5633-2.680.22181450.1924274399
2.68-2.82120.22131470.1842274299
2.8212-2.99790.19861430.1823271399
2.9979-3.22920.23961420.1806269898
3.2292-3.55390.16691390.1633265296
3.5539-4.06750.19171400.143270098
4.0675-5.12220.17061480.14272099
5.1222-35.660.19131360.1772266897
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)
11.9445-0.47391.69912.8587-1.65865.045-0.08150.04610.1658-0.0051-0.0832-0.0387-0.27610.24350.12790.130.002-0.01730.14170.00410.159414.804210.252825.3467
23.6229-1.48-0.11724.74562.84064.96050.0598-0.0194-0.0428-0.1256-0.08780.0728-0.1046-0.18270.02220.14390.04040.01680.15050.00840.1673-3.825318.909725.918
33.25685.10691.03149.4346-0.17576.61430.3871-0.21880.19260.5262-0.22530.32920.2057-0.1585-0.13110.20010.0870.02820.14430.01560.17411.416411.191529.6248
41.7075-0.3951-1.32332.21540.58532.44470.02880.21180.0314-0.1796-0.07150.0902-0.1408-0.19520.04320.12840.0149-0.01130.14820.01140.12997.29752.3587-0.3875
54.6192-2.93910.06152.4375-1.25932.99820.3430.31530.0382-0.4196-0.3111-0.11410.15490.06060.00050.29880.06740.00610.20470.00130.2515-0.598122.7152-1.54
66.42674.8781-2.04269.0887-4.82467.6260.13970.55940.5118-0.59670.11490.1049-0.39760.0961-0.22120.40630.13860.07090.3459-0.0040.35117.837517.6172-6.5293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resid 1 through 78) or (resid 501 through 502))A0
2X-RAY DIFFRACTION2chain 'A' and ((resid 79 through 147) or (resid 504))A0
3X-RAY DIFFRACTION3chain 'C' and (resid 1612 through 1637)C1612 - 1637
4X-RAY DIFFRACTION4chain 'B' and ((resid 2 through 78) or (resid 501 through 502))B0
5X-RAY DIFFRACTION5chain 'B' and ((resid 79 through 146) or (resid 503 through 504))B0
6X-RAY DIFFRACTION6chain 'D' and (resid 1615 through 1639)D1615 - 1639

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