[English] 日本語
Yorodumi
- PDB-9u9d: Bipartite Genetically Encoded Biosensor sG-GECO1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9u9d
TitleBipartite Genetically Encoded Biosensor sG-GECO1
Components
  • Green fluorescent protein
  • Myosin light chain kinase, smooth muscle, deglutamylated form,Green fluorescent protein,Calmodulin-1
KeywordsFLUORESCENT PROTEIN / GFP / bipartite scpFP / sG-GECO1
Function / homology
Function and homology information


tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking ...tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / nitric-oxide synthase binding / presynaptic endocytosis / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / cleavage furrow / regulation of ryanodine-sensitive calcium-release channel activity / adenylate cyclase binding / protein phosphatase activator activity / catalytic complex / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / postsynaptic cytosol / cellular response to interferon-beta / calcium channel inhibitor activity / phosphatidylinositol 3-kinase binding / presynaptic cytosol / stress fiber / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / regulation of heart rate / calyx of Held / response to amphetamine / bioluminescence / adenylate cyclase activator activity / sarcomere / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / regulation of cytokinesis / generation of precursor metabolites and energy / spindle microtubule / calcium channel regulator activity / positive regulation of receptor signaling pathway via JAK-STAT / response to calcium ion / cellular response to type II interferon / Schaffer collateral - CA1 synapse / G2/M transition of mitotic cell cycle / spindle pole / calcium-dependent protein binding / myelin sheath / lamellipodium / growth cone / vesicle / transmembrane transporter binding / calmodulin binding / protein domain specific binding / calcium ion binding / centrosome / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Fibronectin type III domain ...Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / EF-hand domain pair / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin subtype / Immunoglobulin / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Calmodulin-1 / Myosin light chain kinase, smooth muscle / Green fluorescent protein
Similarity search - Component
Biological speciessynthetic construct (others)
Gallus gallus (chicken)
Aequorea victoria (jellyfish)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWen, Y. / Campbell, R.E.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Anal.Chem. / Year: 2025
Title: Bipartite Genetically Encoded Biosensors to Sense Calcium Ion Dynamics at Membrane-Membrane Contact Sites.
Authors: Yamaguchi, I. / Barazzuol, L. / Dematteis, G. / Zhu, W. / Wen, Y. / Drobizhev, M. / Lim, D. / Campbell, R.E. / Cali, T. / Nasu, Y.
History
DepositionMar 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myosin light chain kinase, smooth muscle, deglutamylated form,Green fluorescent protein,Calmodulin-1
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)52,8502
Polymers52,8502
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-12 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.104, 51.104, 201.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Myosin light chain kinase, smooth muscle, deglutamylated form,Green fluorescent protein,Calmodulin-1


Mass: 26684.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Gallus gallus (chicken), (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Rattus norvegicus (Norway rat)
Gene: Mylk, GFP, Calm1, Calm, Cam, Cam1, CaMI / Production host: Escherichia coli (E. coli)
References: UniProt: P11799, UniProt: P42212, UniProt: P0DP29
#2: Protein Green fluorescent protein


Mass: 26165.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 1.24 Å3/Da / Density % sol: 1.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2m sodium malonate dibasic monohydrate, 0.1M Bis-Tris propane pH 8.5, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→36.14 Å / Num. obs: 634405 / % possible obs: 99.89 % / Redundancy: 24.6 % / CC1/2: 0.999 / Net I/σ(I): 19.93
Reflection shellResolution: 1.8→1.87 Å / Num. unique obs: 25780 / CC1/2: 0.626

-
Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→36.14 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 3675 7.8 %
Rwork0.1835 --
obs0.1868 47094 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 0 174 2013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081903
X-RAY DIFFRACTIONf_angle_d1.2042575
X-RAY DIFFRACTIONf_dihedral_angle_d10.213253
X-RAY DIFFRACTIONf_chiral_restr0.08279
X-RAY DIFFRACTIONf_plane_restr0.009333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.50891420.49061674X-RAY DIFFRACTION98
1.83-1.850.39941400.38981667X-RAY DIFFRACTION100
1.85-1.880.39531420.37011657X-RAY DIFFRACTION100
1.88-1.90.36431430.32061716X-RAY DIFFRACTION100
1.9-1.930.36321310.2661627X-RAY DIFFRACTION100
1.93-1.970.25171510.24121703X-RAY DIFFRACTION100
1.97-20.26611350.22351642X-RAY DIFFRACTION100
2-2.040.23271440.2281684X-RAY DIFFRACTION100
2.04-2.080.24641430.20751653X-RAY DIFFRACTION100
2.08-2.120.27091430.21561695X-RAY DIFFRACTION100
2.12-2.160.25911380.22141646X-RAY DIFFRACTION100
2.16-2.210.31081420.22661688X-RAY DIFFRACTION100
2.21-2.270.27251400.20731659X-RAY DIFFRACTION100
2.27-2.330.27961440.19331701X-RAY DIFFRACTION100
2.33-2.40.22811370.19471613X-RAY DIFFRACTION100
2.4-2.480.27521450.21692X-RAY DIFFRACTION100
2.48-2.570.23141360.20051682X-RAY DIFFRACTION100
2.57-2.670.24891410.20551684X-RAY DIFFRACTION100
2.67-2.790.29041430.20761657X-RAY DIFFRACTION100
2.79-2.940.21531400.21651668X-RAY DIFFRACTION100
2.94-3.120.29891340.19261656X-RAY DIFFRACTION100
3.12-3.360.23391450.17381687X-RAY DIFFRACTION100
3.36-3.70.19081440.17281674X-RAY DIFFRACTION100
3.7-4.230.17211470.14591669X-RAY DIFFRACTION100
4.23-5.330.1841430.12811647X-RAY DIFFRACTION100
5.34-36.140.18931420.16691678X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 50.4424 Å / Origin y: 13.3702 Å / Origin z: 88.6475 Å
111213212223313233
T0.2829 Å2-0.0009 Å20.0086 Å2-0.2643 Å2-0.0117 Å2--0.2941 Å2
L1.3868 °20.4085 °20.3613 °2-3.8099 °21.2065 °2--2.7071 °2
S0.0427 Å °0.0435 Å °0.0378 Å °0.4618 Å °0.0057 Å °0.0687 Å °0.1873 Å °0.0432 Å °-0.0427 Å °
Refinement TLS groupSelection details: all

+
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