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- PDB-4oy4: calcium-free CaMPARI v0.2 -

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Basic information

Entry
Database: PDB / ID: 4oy4
Titlecalcium-free CaMPARI v0.2
ComponentsChimera protein of Calmodulin, GPF-like protein EosFP, and Myosin light chain kinase
KeywordsCalcium Binding / Fluorescent / Transferase / calcium / fluorescent protein / photoconversion / integrator / engineered protein
Function / homology
Function and homology information


regulation of store-operated calcium channel activity / : / regulation of high voltage-gated calcium channel activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : ...regulation of store-operated calcium channel activity / : / regulation of high voltage-gated calcium channel activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / positive regulation of DNA binding / negative regulation of high voltage-gated calcium channel activity / nitric-oxide synthase binding / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / calcineurin-mediated signaling / regulation of synaptic vesicle endocytosis / protein phosphatase activator activity / postsynaptic cytosol / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / phosphatidylinositol 3-kinase binding / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / activation of adenylate cyclase activity / enzyme regulator activity / regulation of calcium-mediated signaling / titin binding / voltage-gated potassium channel complex / calcium channel regulator activity / potassium ion transmembrane transport / sperm midpiece / calcium channel complex / calyx of Held / nitric-oxide synthase regulator activity / response to amphetamine / positive regulation of nitric-oxide synthase activity / adenylate cyclase activator activity / regulation of heart rate / bioluminescence / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / generation of precursor metabolites and energy / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / calcium-mediated signaling / Schaffer collateral - CA1 synapse / cellular response to type II interferon / response to calcium ion / spindle pole / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / disordered domain specific binding / kinase activity / myelin sheath / growth cone / protein autophosphorylation / vesicle / transmembrane transporter binding / calmodulin binding / neuron projection / positive regulation of apoptotic process / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Immunoglobulin subtype 2 ...Green Fluorescent Protein / Green fluorescent protein / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / EF-hand domain pair / 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 / Immunoglobulin-like fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-1 / Green to red photoconvertible GFP-like protein EosFP / Myosin light chain kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Lobophyllia hemprichii (invertebrata)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å
AuthorsFosque, B.F. / Schreiter, E.R.
CitationJournal: Science / Year: 2015
Title: Neural circuits. Labeling of active neural circuits in vivo with designed calcium integrators.
Authors: Fosque, B.F. / Sun, Y. / Dana, H. / Yang, C.T. / Ohyama, T. / Tadross, M.R. / Patel, R. / Zlatic, M. / Kim, D.S. / Ahrens, M.B. / Jayaraman, V. / Looger, L.L. / Schreiter, E.R.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_torsion / refine_hist / struct_conn / struct_keywords
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_keywords.text
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimera protein of Calmodulin, GPF-like protein EosFP, and Myosin light chain kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6655
Polymers47,2891
Non-polymers3764
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.670, 68.670, 172.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Chimera protein of Calmodulin, GPF-like protein EosFP, and Myosin light chain kinase / CaM


Mass: 47289.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Lobophyllia hemprichii (invertebrata), (gene. exp.) Gallus gallus (chicken)
Gene: Calm1, Calm, Cam, Cam1, Calm2, Cam2, Camb, Calm3, Cam3, Camc
Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express
References: UniProt: P62161, UniProt: Q5S6Z9, UniProt: Q6LDG3, UniProt: P0DP29*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350, 10 mM EGTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→57.59 Å / Num. obs: 27700 / % possible obs: 99.9 % / Redundancy: 7.5 % / Net I/σ(I): 13.4

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementResolution: 2.03→53.75 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.715 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23519 1389 5 %RANDOM
Rwork0.19613 ---
obs0.1981 26240 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.229 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.03→53.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 22 104 2854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192827
X-RAY DIFFRACTIONr_bond_other_d0.0030.022617
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.9663804
X-RAY DIFFRACTIONr_angle_other_deg0.9563.0026049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1865336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42924.326141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17415507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8291516
X-RAY DIFFRACTIONr_chiral_restr0.1150.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.029→2.082 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 85 -
Rwork0.216 1901 -
obs--99.2 %

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