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- PDB-7cqp: Complex of TRPC4 and Calmodulin_Nlobe -

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Basic information

Entry
Database: PDB / ID: 7cqp
TitleComplex of TRPC4 and Calmodulin_Nlobe
Components
  • Calmodulin-1
  • Peptide from Short transient receptor potential channel 4
KeywordsSIGNALING PROTEIN / Calmodulin / TRP channel
Function / homology
Function and homology information


CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / Synthesis of IP3 and IP4 in the cytosol / CLEC7A (Dectin-1) induces NFAT activation ...CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / Synthesis of IP3 and IP4 in the cytosol / CLEC7A (Dectin-1) induces NFAT activation / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Ion transport by P-type ATPases / Calcineurin activates NFAT / Unblocking of NMDA receptors, glutamate binding and activation / Protein methylation / RAF activation / VEGFR2 mediated vascular permeability / RAS processing / gamma-aminobutyric acid secretion / FCERI mediated Ca+2 mobilization / Ca2+ pathway / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / RAF/MAP kinase cascade / store-operated calcium channel activity / PKA activation / Smooth Muscle Contraction / Platelet degranulation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / TRP channels / Stimuli-sensing channels / inositol 1,4,5 trisphosphate binding / Ion homeostasis / calcium ion import / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / cortical cytoskeleton / negative regulation of ryanodine-sensitive calcium-release channel activity / oligodendrocyte differentiation / calcineurin-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / calyx of Held / adenylate cyclase activator activity / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / beta-catenin binding / caveola / cellular response to type II interferon / spindle pole / G2/M transition of mitotic cell cycle / cell-cell junction / myelin sheath / basolateral plasma membrane / transmembrane transporter binding / cadherin binding / membrane raft / centrosome / calcium ion binding / protein kinase binding / cell surface / protein-containing complex / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Transient receptor potential channel, canonical 4 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / EF-hand / : / Recoverin; domain 1 / Ankyrin repeat / EF-hand domain pair ...Transient receptor potential channel, canonical 4 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / EF-hand / : / Recoverin; domain 1 / Ankyrin repeat / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / EF-hand, calcium binding motif / Ankyrin repeat-containing domain superfamily / 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 / Short transient receptor potential channel 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsShen, Z.S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670765 China
National Natural Science Foundation of China (NSFC)31870746 China
CitationJournal: Structure / Year: 2021
Title: Calmodulin binds to Drosophila TRP with an unexpected mode.
Authors: Chen, W. / Shen, Z. / Asteriti, S. / Chen, Z. / Ye, F. / Sun, Z. / Wan, J. / Montell, C. / Hardie, R.C. / Liu, W. / Zhang, M.
History
DepositionAug 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Calmodulin-1
C: Peptide from Short transient receptor potential channel 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3154
Polymers12,2352
Non-polymers802
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-43 kcal/mol
Surface area5250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.460, 64.460, 120.751
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-226-

HOH

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Components

#1: Protein Calmodulin-1


Mass: 8868.894 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Calm1, Calm, Cam, Cam1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP26
#2: Protein/peptide Peptide from Short transient receptor potential channel 4 / TrpC4 / Capacitative calcium entry channel Trp4 / Receptor-activated cation channel TRP4


Mass: 3365.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9QUQ5
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 55.7% w/v Polyethylene glycol 1000, 150mM MES, 2% v/v 2-Methyl-2,4-pentanediol, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 12754 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.039 / Rrim(I) all: 0.11 / Χ2: 0.938 / Net I/σ(I): 5.6 / Num. measured all: 330733
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.937.51.00421880.7680.3861.0760.83799.5
1.93-1.977.61.00122520.7540.3831.0730.8399.6
1.97-2.017.50.76922070.8120.2960.8250.89199.7
2.01-2.057.50.65322240.8770.2510.70.92999.6
2.05-2.097.50.54822550.8980.2110.5880.92699.3
2.09-2.147.50.48922490.9270.190.5240.92299.8
2.14-2.197.40.39621850.9420.1540.4260.98999.8
2.19-2.257.40.33422530.9550.1310.3591.0899.7
2.25-2.327.20.27722530.9620.110.2981.05100
2.32-2.396.50.24722300.960.1040.2691.07999.1
2.39-2.487.30.22421970.9730.0880.2411.07499.9
2.48-2.587.80.1922340.9790.0720.2031.08199.9
2.58-2.77.70.15822720.9840.060.1691.086100
2.7-2.847.60.14322140.9870.0550.1531.105100
2.84-3.027.60.11722100.990.0450.1261.051100
3.02-3.257.30.10222630.9920.040.110.993100
3.25-3.586.60.08122460.9940.0340.0880.88799.6
3.58-4.097.90.06822260.9960.0260.0730.76100
4.09-5.167.70.0622340.9960.0230.0640.641100
5.16-507.30.05722470.9970.0220.0610.57199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3228refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1up5

1up5


Resolution: 1.9→40.988 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 607 4.96 %
Rwork0.2194 11637 -
obs0.221 12244 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.34 Å2 / Biso mean: 27.54 Å2 / Biso min: 16.17 Å2
Refinement stepCycle: final / Resolution: 1.9→40.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms725 0 2 30 757
Biso mean--24.2 28.56 -
Num. residues----95
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-2.09120.28181400.2358280099
2.0912-2.39380.22831350.2299285799
2.3938-3.01580.24021460.23652915100
3.0158-40.9880.2541860.20553065100

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