[English] 日本語
Yorodumi
- PDB-7cqh: Complex of TRP_CBS2 and Calmodulin_Clobe -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cqh
TitleComplex of TRP_CBS2 and Calmodulin_Clobe
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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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 / Transient receptor potential channel


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more