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- PDB-6daf: 2.4 Angstrom crystal structure of the F141L Ca/CaM:CaV1.2 IQ doma... -

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Basic information

Entry
Database: PDB / ID: 6daf
Title2.4 Angstrom crystal structure of the F141L Ca/CaM:CaV1.2 IQ domain complex
Components
  • Calmodulin-1
  • Voltage-dependent L-type calcium channel subunit alpha-1C
KeywordsCALCIUM BINDING PROTEIN/MEMBRANE PROTEIN / calmodulin / mutant / complex / 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 / NCAM1 interactions / camera-type eye development / 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 / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / 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 NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / alpha-actinin binding / RHO GTPases activate PAKs / calcineurin-mediated signaling / 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 / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / 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 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / 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: 2.4 Å
AuthorsWang, K. / Van Petegem, F.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Arrhythmia mutations in calmodulin cause conformational changes that affect interactions with the cardiac voltage-gated calcium channel.
Authors: Wang, K. / Holt, C. / Lu, J. / Brohus, M. / Larsen, K.T. / Overgaard, M.T. / Wimmer, R. / Van Petegem, F.
History
DepositionMay 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.4Oct 4, 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)42,33312
Polymers42,0134
Non-polymers3218
Water34219
1
A: Calmodulin-1
C: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1676
Polymers21,0062
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-77 kcal/mol
Surface area8260 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)21,1676
Polymers21,0062
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-79 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.355, 121.309, 125.897
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: 16687.334 Da / Num. of mol.: 2 / Mutation: F141L
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 / Fragment: UNP residues 1611-1644
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.5 M potassium nitrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→43.678 Å / Num. obs: 39395 / % possible obs: 99.1 % / Redundancy: 3.09 % / Biso Wilson estimate: 60.44 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.057 / Net I/σ(I): 13.31
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
2.4-2.552.4363450.8690.523198.8
2.55-2.721
2.72-2.941
2.94-3.221
3.22-3.591
3.59-4.151
4.15-5.071
5.07-7.121
7.12-43.6781

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BE6

2be6


Resolution: 2.4→43.678 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.4
RfactorNum. reflection% reflection
Rfree0.243 1974 5.01 %
Rwork0.203 --
obs0.205 39391 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.52 Å2 / Biso mean: 78.8418 Å2 / Biso min: 35.37 Å2
Refinement stepCycle: final / Resolution: 2.4→43.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 8 19 2490
Biso mean--70.8 59.8 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4004-2.46040.34161450.29082676282197
2.4604-2.5270.35071370.261526592796100
2.527-2.60130.33341400.246226752815100
2.6013-2.68530.30941480.239727142862100
2.6853-2.78120.26661410.227226902831100
2.7812-2.89250.22351450.22952676282199
2.8925-3.02420.27761330.22632641277499
3.0242-3.18360.33161440.238727232867100
3.1836-3.3830.24871420.21722663280599
3.383-3.6440.28371400.21252645278599
3.644-4.01050.21121360.1852647278399
4.0105-4.59030.20321410.16412662280399
4.5903-5.78120.22771420.19572709285199
5.7812-43.68490.21511400.19312637277798
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)
18.09321.2906-0.04483.9637-0.62718.4610.06110.0620.35320.4994-0.3471-0.6151-0.99830.98380.21350.7261-0.0605-0.06090.80560.31090.721510.259311.515437.014
25.2189-1.7239-1.06919.1986-2.85987.0234-0.1859-0.3837-0.65690.4488-0.1298-0.06750.3132-0.3340.35980.57630.06840.01030.54070.02120.45131.488714.946416.3527
32.981-0.4373-2.23814.67570.29012.6672-0.6254-0.1905-0.410.15650.10480.11361.4016-0.3810.45680.83170.010.130.85570.36040.78252.25648.124524.8508
47.56310.26151.30518.21674.52379.1945-0.0416-0.5688-0.09270.91220.3925-0.73930.82350.8258-0.34220.63440.1809-0.08180.7212-0.27370.731718.44611.2889-9.8747
58.32644.4286-4.81737.5458-0.91339.6272-0.09360.528-0.27590.0260.1441-0.2163-0.4911-0.6099-0.0550.4230.0722-0.02470.3889-0.09280.376410.635720.8748-2.9053
67.6087-0.84640.93259.3978-3.14556.6999-0.15230.7544-0-0.9074-0.04040.71330.104-0.56540.12680.5040.0423-0.09540.6345-0.24120.535610.806514.6494-11.6103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resid 3 through 78 ) or (resid 501 through 502))A0
2X-RAY DIFFRACTION2chain 'A' and ((resid 79 through 146 ) or (resid 503 through 504))A0
3X-RAY DIFFRACTION3chain 'C' and (resid 1616 through 1634 )C0
4X-RAY DIFFRACTION4chain 'B' and ((resid 3 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 1637 )D0

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