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- PDB-6u3d: 1.75 Angstrom crystal structure of the N53I Ca-CaM:CaV1.2 IQ doma... -

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Basic information

Entry
Database: PDB / ID: 6u3d
Title1.75 Angstrom crystal structure of the N53I 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 / membrane depolarization during atrial cardiac muscle cell action potential / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / membrane depolarization during AV node cell action potential / positive regulation of adenylate cyclase activity / cardiac conduction ...: / 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 / membrane depolarization during atrial cardiac muscle cell action potential / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / membrane depolarization during AV node cell action potential / positive regulation of adenylate cyclase activity / cardiac conduction / L-type voltage-gated calcium channel complex / membrane depolarization during cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / regulation of ventricular cardiac muscle cell action potential / high voltage-gated calcium channel activity / camera-type eye development / NCAM1 interactions / embryonic forelimb morphogenesis / CaM pathway / Cam-PDE 1 activation / calcium ion transport into cytosol / Sodium/Calcium exchangers / cell communication by electrical coupling involved in cardiac conduction / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / 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 / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / Activation of RAC1 downstream of NMDARs / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / autophagosome membrane docking / voltage-gated calcium channel complex / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / regulation of heart rate by cardiac conduction / alpha-actinin binding / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / calcium ion import across plasma membrane / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / voltage-gated calcium channel activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / 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 / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / Regulation of insulin secretion / Translocation of SLC2A4 (GLUT4) to the plasma membrane
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 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
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: 1.75 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 / struct_conn
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

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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)42,39912
Polymers42,0794
Non-polymers3218
Water3,909217
1
A: Calmodulin-1
C: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2006
Polymers21,0392
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-78 kcal/mol
Surface area9120 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)21,2006
Polymers21,0392
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-78 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.400, 43.369, 66.962
Angle α, β, γ (deg.)90.000, 111.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-1 /


Mass: 16720.404 Da / Num. of mol.: 2 / Mutation: N53I
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.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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 Å3/Da / Density % sol: 38.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 56097 / % possible obs: 89.6 % / Redundancy: 1.72 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.55
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.75-1.8670290.8831
5.2-35.5621790.9971

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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: 6DAF

6daf


Resolution: 1.75→35.56 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.11 / Phase error: 20.23
RfactorNum. reflection% reflection
Rfree0.2009 2804 5 %
Rwork0.1636 --
obs0.1654 56089 89.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.22 Å2 / Biso mean: 29.2617 Å2 / Biso min: 11.54 Å2
Refinement stepCycle: final / Resolution: 1.75→35.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 8 217 2927
Biso mean--22.32 34.99 -
Num. residues----349
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7503-1.78050.3461920.3314174959
1.7805-1.81280.30011030.2791203768
1.8128-1.84770.30121130.2291224777
1.8477-1.88540.23051480.212267889
1.8854-1.92640.2281440.2053275594
1.9264-1.97120.25591450.1994291197
1.9712-2.02050.23021500.1905281597
2.0205-2.07510.2151460.1851285296
2.0751-2.13620.21051470.1774276594
2.1362-2.20510.24471480.1697284695
2.2051-2.28390.19611550.1578287795
2.2839-2.37540.20031460.1612278995
2.3754-2.48350.19491490.1713277294
2.4835-2.61430.25471530.175271492
2.6143-2.77810.19631410.1641276094
2.7781-2.99250.17981460.1742280294
2.9925-3.29340.17851450.1672276092
3.2934-3.76950.19141400.1354270691
3.7695-4.74740.16011440.1204271992
4.7474-35.560.18271490.1553273192
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)
12.0220.00210.20431.47740.16664.576-0.1008-0.08320.08540.082-0.0749-0.1366-0.02710.35950.14810.1253-0.0058-0.01470.16060.04470.18081.0372-1.9032-27.6007
24.08390.01971.30712.4334-0.07831.7384-0.01870.14620.0731-0.0118-0.00490.0314-0.0201-0.06550.03040.1267-0.01730.01940.09220.00930.1014-12.8045-18.3652-22.009
34.86482.60754.32762.49951.39024.65840.29820.1648-0.55150.1080.0154-0.2030.24490.2014-0.25670.16370.00970.02650.12940.00930.1681-8.7137-13.0735-31.579
44.38020.1362-0.83721.3317-0.63971.6612-0.06840.1421-0.2505-0.0490.0523-0.0170.0316-0.08690.00610.1555-0.02940.01160.1531-0.06750.15413.7507-21.3578-13.4086
53.28870.06420.99542.3809-0.11513.62390.09810.0471-0.04610.0135-0.0338-0.06290.08480.2512-0.05420.18190.00150.01960.1697-0.08360.185118.7834-5.291.1854
64.25522.40353.81342.15241.41554.0846-0.0560.0320.2940.1107-0.042-0.08130.08210.11450.09940.20610.02430.01860.1785-0.05380.168923.5275-11.315-5.374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resid 2 through 78) or (resid 501 through 502))A0
2X-RAY DIFFRACTION2chain 'A' and ((resid 79 through 147) or (resid 503 through 504))A0
3X-RAY DIFFRACTION3chain 'C' and (resid 1611 through 1638)C1611 - 1638
4X-RAY DIFFRACTION4chain 'B' and ((resid 2 through 78) or (resid 501 through 502))B0
5X-RAY DIFFRACTION5chain 'B' and ((resid 79 through 147) or (resid 503 through 504))B0
6X-RAY DIFFRACTION6chain 'D' and (resid 1612 through 1640)D1612 - 1640

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