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- PDB-9u9d: Bipartite Genetically Encoded Biosensor sG-GECO1 -

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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 / positive regulation of sarcomere organization / positive regulation of striated muscle contraction / transporter inhibitor activity / : / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / cardiac muscle cell development ...tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / positive regulation of sarcomere organization / positive regulation of striated muscle contraction / transporter inhibitor activity / : / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / cardiac muscle cell development / response to corticosterone / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / : / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle cell action potential / presynaptic endocytosis / cleavage furrow / calcineurin-mediated signaling / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / adenylate cyclase binding / protein phosphatase activator activity / regulation of synaptic vesicle endocytosis / detection of calcium ion / postsynaptic cytosol / regulation of cardiac muscle contraction / cell surface receptor signaling pathway via JAK-STAT / catalytic complex / phosphatidylinositol 3-kinase binding / heart morphogenesis / calcium channel inhibitor activity / presynaptic cytosol / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / stress fiber / titin binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / regulation of heart rate / calyx of Held / nitric-oxide synthase regulator activity / bioluminescence / adenylate cyclase activator activity / regulation of cytokinesis / protein serine/threonine kinase activator activity / spindle microtubule / sarcomere / positive regulation of receptor signaling pathway via JAK-STAT / response to amphetamine / generation of precursor metabolites and energy / calcium channel regulator activity / response to calcium ion / cellular response to type II interferon / G2/M transition of mitotic cell cycle / Schaffer collateral - CA1 synapse / spindle pole / calcium-dependent protein binding / myelin sheath / lamellipodium / synaptic vesicle membrane / growth cone / sperm midpiece / vesicle / transmembrane transporter binding / calmodulin binding / protein domain specific binding / calcium ion binding / centrosome / protein kinase binding / chromatin / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytoplasm / cytosol
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 / : / Fibronectin type III domain / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein ...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 / : / Fibronectin type III domain / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / EF-hand domain pair / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Revision 2.0Mar 18, 2026Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 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

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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

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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

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