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- PDB-7cqv: Complex of TRP_CBS1 and Calmodulin_Nlobe -

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Basic information

Entry
Database: PDB / ID: 7cqv
TitleComplex of TRP_CBS1 and Calmodulin_Nlobe
Components
  • AT15141p
  • Transient receptor potential proteinTransient receptor potential channel
KeywordsSIGNALING PROTEIN / Calmodulin / TRP channel
Function / homology
Function and homology information


rhabdomere microvillus membrane / : / Ion homeostasis / TRP channels / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / detection of light stimulus involved in sensory perception / inaD signaling complex / light-activated monoatomic ion channel activity / cellular response to anoxia / rhabdomere ...rhabdomere microvillus membrane / : / Ion homeostasis / TRP channels / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / detection of light stimulus involved in sensory perception / inaD signaling complex / light-activated monoatomic ion channel activity / cellular response to anoxia / rhabdomere / detection of light stimulus involved in visual perception / store-operated calcium channel activity / cation channel complex / olfactory learning / phototransduction, visible light / inositol 1,4,5 trisphosphate binding / retina homeostasis / inorganic cation transmembrane transport / response to light stimulus / phototransduction / regulation of cytosolic calcium ion concentration / mitochondrion organization / calcium-mediated signaling / calcium ion transmembrane transport / sensory perception of sound / calcium channel activity / protein localization / calcium ion transport / sensory perception of smell / calmodulin binding / protein heterodimerization activity / calcium ion binding / protein homodimerization activity / membrane / identical protein binding / plasma membrane
Similarity search - Function
Calmodulin / Transient receptor ion channel II / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeat / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...Calmodulin / Transient receptor ion channel II / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeat / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / Ion transport domain / Ion transport protein / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
AT15141p / Transient receptor potential protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 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

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Assembly

Deposited unit
E: AT15141p
A: AT15141p
B: Transient receptor potential protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2527
Polymers27,0913
Non-polymers1604
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-79 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.449, 98.449, 134.263
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11E-237-

HOH

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Components

#1: Protein AT15141p / Calmodulin_Nlobe


Mass: 8868.894 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Cam-RB / Production host: Escherichia coli (E. coli) / References: UniProt: C6SUZ2
#2: Protein Transient receptor potential protein / Transient receptor potential channel


Mass: 9353.659 Da / Num. of mol.: 1 / Fragment: CBS1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: trp, CG7875 / Production host: Escherichia coli (E. coli) / References: UniProt: P19334
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 2.5M Ammonium sulfate, 0.1M BIS-TRIS propane pH 7.0

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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: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 24105 / % possible obs: 100 % / Redundancy: 19.6 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.014 / Rrim(I) all: 0.063 / Χ2: 1.803 / Net I/σ(I): 8.6 / Num. measured all: 473415
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.8119.50.35611920.9820.0820.3650.457100
1.81-1.8420.30.30311930.9880.0690.3110.471100
1.84-1.8820.20.24311870.9880.0560.250.571100
1.88-1.92200.21311870.9930.0490.2180.548100
1.92-1.9619.90.17912160.9940.0410.1840.577100
1.96-219.40.15411950.9940.0360.1580.711100
2-2.05180.1311830.9940.0310.1340.754100
2.05-2.1119.70.1211820.9940.0280.1230.849100
2.11-2.1720.50.10511850.9940.0240.1070.934100
2.17-2.2420.30.08512150.9980.0190.0880.723100
2.24-2.3219.90.0811840.9960.0180.0830.844100
2.32-2.4219.40.07612030.9970.0180.0781.14100
2.42-2.5317.90.06812100.9980.0160.071.149100
2.53-2.6620.50.06212090.9990.0140.0631.116100
2.66-2.8320.30.05411910.9980.0120.0551.004100
2.83-3.04200.05212080.9980.0120.0541.885100
3.04-3.3518.50.04812180.9960.0110.052.735100
3.35-3.8320.70.04112220.9980.0090.0422.692100
3.83-4.8318.80.04112370.9970.010.0423.60299.9
4.83-5019.10.06312880.9940.0150.06512.83399.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1up5

1up5


Resolution: 1.78→49.22 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1202 4.99 %
Rwork0.2048 22889 -
obs0.2063 24091 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.67 Å2 / Biso mean: 30.8974 Å2 / Biso min: 9.52 Å2
Refinement stepCycle: final / Resolution: 1.78→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 4 73 1521
Biso mean--17.89 27.85 -
Num. residues----195
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.850.27521270.223325302657100
1.85-1.940.22741170.195925172634100
1.94-2.040.22971370.194125152652100
2.04-2.170.18951330.19725102643100
2.17-2.340.23061510.197325222673100
2.34-2.570.21361340.215825362670100
2.57-2.940.27181410.220425282669100
2.94-3.710.23071310.216725812712100
3.71-49.220.23611310.19112650278199

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