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- PDB-7cqh: Complex of TRP_CBS2 and Calmodulin_Clobe -

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Basic information

Entry
Database: PDB / ID: 7cqh
TitleComplex of TRP_CBS2 and Calmodulin_Clobe
Components
  • AT15141p
  • Transient receptor potential protein
KeywordsSIGNALING PROTEIN / Calmodulin / TRP channel
Function / homology
Function and homology information


phospholipase C-activating opsin-mediated signaling pathway / Ion homeostasis / TRP channels / rhabdomere microvillus membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / detection of light stimulus involved in sensory perception / inaD signaling complex / cellular response to anoxia / rhabdomere / store-operated calcium channel activity ...phospholipase C-activating opsin-mediated signaling pathway / Ion homeostasis / TRP channels / rhabdomere microvillus membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / detection of light stimulus involved in sensory perception / inaD signaling complex / cellular response to anoxia / rhabdomere / store-operated calcium channel activity / detection of light stimulus involved in visual perception / olfactory learning / inositol 1,4,5 trisphosphate binding / cation channel complex / retina homeostasis / : / response to light stimulus / phototransduction, visible light / phototransduction / regulation of cytosolic calcium ion concentration / mitochondrion organization / sensory perception of sound / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / sensory perception of smell / intracellular protein localization / calmodulin binding / protein heterodimerization activity / calcium ion binding / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
Transient receptor ion channel domain / Transient receptor ion channel II / 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. ...Transient receptor ion channel domain / Transient receptor ion channel II / 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 / 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
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: 2.15 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 10, 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
B: AT15141p
A: Transient receptor potential protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3124
Polymers13,2322
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-40 kcal/mol
Surface area5340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.344, 58.344, 92.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein AT15141p / CaM_Clobe


Mass: 8282.970 Da / Num. of mol.: 1
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/peptide Transient receptor potential protein


Mass: 4948.654 Da / Num. of mol.: 1 / Fragment: CBS2
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.: 2 / Source method: obtained synthetically / Formula: Ca
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: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 11.4% w/v Polyethyleneglycol 20000, 150mM Sodium acetate, 7% v/v Ethyleneglycol, pH 4.5

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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: 2.15→50 Å / Num. obs: 8342 / % possible obs: 99.1 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.014 / Rrim(I) all: 0.052 / Χ2: 0.616 / Net I/σ(I): 7.3 / Num. measured all: 105408
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.199.10.3683690.9820.1190.3880.4488.5
2.19-2.239.50.333970.9890.1060.3480.43496.6
2.23-2.2710.30.273910.9970.0840.2840.44496.8
2.27-2.3211.30.34340.9940.0910.3140.44599.8
2.32-2.3712.30.2564330.9960.0750.2670.4599.5
2.37-2.4212.90.2883990.9940.0830.30.438100
2.42-2.48120.2284330.9960.0680.2380.456100
2.48-2.5512.70.2034080.9960.0590.2120.467100
2.55-2.6213.90.12340410.0350.1280.471100
2.62-2.71140.1244510.9980.0340.1290.512100
2.71-2.8113.70.1024210.9990.0290.1060.526100
2.81-2.9213.80.094160.9990.0250.0930.547100
2.92-3.0513.70.0814030.9990.0230.0840.604100
3.05-3.2112.70.0634220.9990.0180.0660.641100
3.21-3.41130.0524320.9990.0150.0540.726100
3.41-3.6814.20.0464170.9990.0130.0480.742100
3.68-4.05140.0434220.9990.0120.0450.817100
4.05-4.63130.0394220.9990.0110.040.848100
4.63-5.8313.20.044270.9990.0110.0410.8899.8
5.83-5012.80.0454410.9980.0130.0471.16699.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.12refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1up5

1up5


Resolution: 2.15→49.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.048 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 415 5 %RANDOM
Rwork0.214 ---
obs0.2158 7910 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.74 Å2 / Biso mean: 69.357 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-3.71 Å2-0 Å20 Å2
2--3.71 Å20 Å2
3----7.42 Å2
Refinement stepCycle: final / Resolution: 2.15→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms690 0 2 0 692
Biso mean--63.35 --
Num. residues----92
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 34 -
Rwork0.362 513 -
all-547 -
obs--90.71 %

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