[English] 日本語
Yorodumi
- PDB-9vsj: Crystal structure of the genetically-encoded green calcium sensor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vsj
TitleCrystal structure of the genetically-encoded green calcium sensor icBTnC2 in its calcium bound-state
ComponentsicBTnC2 - the genetically-encoded green calcium sensor based on the fluorescent protein mBaoJin and calcium binding domain of C-terminal minimal domain of troponin C from Calypte Anna
KeywordsFLUORESCENT PROTEIN / mBaoJin2 / green fluorescent protein / indicator / sensor / calcium
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Dorovatovskii, P.V. / Vlaskina, A.V. / Agapova, Y.K. / Petrenko, D.E. / Subach, O.M. / Chelykhova, S.A. / Popov, V.O. / Subach, F.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation Russian Federation
CitationJournal: To Be Published
Title: Crystal structure of the genetically-encoded green calcium sensor icBTnC2 in its calcium bound-state
Authors: Boyko, K.M. / Nikolaeva, A.Y. / Dorovatovskii, P.V. / Vlaskina, A.V. / Agapova, Y.K. / Petrenko, D.E. / Subach, O.M. / Chelykhova, S.A. / Popov, V.O. / Subach, F.V.
History
DepositionJul 8, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: icBTnC2 - the genetically-encoded green calcium sensor based on the fluorescent protein mBaoJin and calcium binding domain of C-terminal minimal domain of troponin C from Calypte Anna
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3205
Polymers35,0981
Non-polymers2224
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.697, 128.697, 52.737
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-721-

HOH

-
Components

#1: Protein icBTnC2 - the genetically-encoded green calcium sensor based on the fluorescent protein mBaoJin and calcium binding domain of C-terminal minimal domain of troponin C from Calypte Anna


Mass: 35098.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.76 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 30% MPD,20mM CaCl2 ,100 mM NaAcetate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.75172 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 17, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75172 Å / Relative weight: 1
ReflectionResolution: 1.55→55.73 Å / Num. obs: 72730 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.973 / Net I/σ(I): 6.7
Reflection shellResolution: 1.55→1.58 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3537 / CC1/2: 0.53

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimless0.8.2data scaling
DIALS3.21data reduction
gemmi0.7.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→55.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.275 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21958 3647 5 %RANDOM
Rwork0.19736 ---
obs0.19847 69063 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.069 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20 Å2
2---0.09 Å20 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.55→55.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 10 248 2625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122506
X-RAY DIFFRACTIONr_bond_other_d0.0060.0162216
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.8343379
X-RAY DIFFRACTIONr_angle_other_deg1.0341.7665149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8835309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.002516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55310410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022921
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02561
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3091208
X-RAY DIFFRACTIONr_mcbond_other4.3091207
X-RAY DIFFRACTIONr_mcangle_it6.0351504
X-RAY DIFFRACTIONr_mcangle_other6.0331505
X-RAY DIFFRACTIONr_scbond_it6.8921298
X-RAY DIFFRACTIONr_scbond_other6.891299
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.4114.1171869
X-RAY DIFFRACTIONr_long_range_B_refined10.37410905
X-RAY DIFFRACTIONr_long_range_B_other10.37810687
X-RAY DIFFRACTIONr_rigid_bond_restr5.94231387
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 279 -
Rwork0.27 5062 -
obs--100 %

+
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