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- PDB-4i2y: Crystal Structure of the genetically encoded calcium indicator RGECO1 -

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Basic information

Entry
Database: PDB / ID: 4i2y
TitleCrystal Structure of the genetically encoded calcium indicator RGECO1
ComponentsRGECO1
KeywordsFLUORESCENT PROTEIN / Calcium binding / sensor / mApple / fluorescent calcium indicator
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 / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane ...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 / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / protein phosphatase activator activity / calcium channel regulator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / positive regulation of DNA binding / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / potassium ion transmembrane transport / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / bioluminescence / sarcomere / regulation of cytokinesis / generation of precursor metabolites and energy / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / spindle microtubule / spindle pole / response to calcium ion / calcium-dependent protein binding / disordered domain specific binding / G2/M transition of mitotic cell cycle / myelin sheath / kinase activity / growth cone / vesicle / transmembrane transporter binding / protein autophosphorylation / neuron projection / positive regulation of apoptotic process / protein domain specific binding / phosphorylation / 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 / Immunoglobulin C-2 Type ...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 / Myosin light chain kinase / Red fluorescent protein drFP583
Similarity search - Component
Biological speciesGallus gallus (chicken)
Discosoma sp. (sea anemone)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAkerboom, J. / Looger, L.L. / Schreiter, E.R.
CitationJournal: Front Mol Neurosci / Year: 2013
Title: Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics.
Authors: Akerboom, J. / Carreras Calderon, N. / Tian, L. / Wabnig, S. / Prigge, M. / Tolo, J. / Gordus, A. / Orger, M.B. / Severi, K.E. / Macklin, J.J. / Patel, R. / Pulver, S.R. / Wardill, T.J. / ...Authors: Akerboom, J. / Carreras Calderon, N. / Tian, L. / Wabnig, S. / Prigge, M. / Tolo, J. / Gordus, A. / Orger, M.B. / Severi, K.E. / Macklin, J.J. / Patel, R. / Pulver, S.R. / Wardill, T.J. / Fischer, E. / Schuler, C. / Chen, T.W. / Sarkisyan, K.S. / Marvin, J.S. / Bargmann, C.I. / Kim, D.S. / Kugler, S. / Lagnado, L. / Hegemann, P. / Gottschalk, A. / Schreiter, E.R. / Looger, L.L.
History
DepositionNov 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RGECO1
B: RGECO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,38110
Polymers95,0602
Non-polymers3218
Water1,78399
1
A: RGECO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6915
Polymers47,5301
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RGECO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6915
Polymers47,5301
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.160, 91.730, 68.570
Angle α, β, γ (deg.)90.00, 95.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RGECO1 / myosin light chain kinase / green fluorescent protein / calmodulin chimera


Mass: 47530.219 Da / Num. of mol.: 2
Mutation: Q44N, T46A, T62S, L65M, R68E, V71A, G74S, H77K, A79G, K81R, L89A, V90A, F92V, S94T, I95T, M97K, Y107A, Y109I, S112I, T117V, Y129C, T132A, R174H, T178S, G197A, H198F, N199Q, V201A, V228A, ...Mutation: Q44N, T46A, T62S, L65M, R68E, V71A, G74S, H77K, A79G, K81R, L89A, V90A, F92V, S94T, I95T, M97K, Y107A, Y109I, S112I, T117V, Y129C, T132A, R174H, T178S, G197A, H198F, N199Q, V201A, V228A, V230I, K240F, K249R, V261I, V262I, T263H, T265N, C274V, F281L, I282R, V284T, S288P, N363D, I366F, K380N, S404G, N414D, E430V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Discosoma sp. (sea anemone), (gene. exp.) Rattus norvegicus (Norway rat)
Production host: Escherichia coli (E. coli)
References: UniProt: Q6LDG3, UniProt: Q9U6Y8, UniProt: P62161
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED EXPRESSION TAG, RESIDUES 37-55 OF ...THIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED EXPRESSION TAG, RESIDUES 37-55 OF UNP Q6LDG3, AN ENGINEERED PVV LINKER, RESIDUES 147-221 OF UNP Q9U6Y8, AN ENGINEERED STGGMDELYKGGTGGSLVSKGEEDNMAI LINKER, RESIDUES 8-145 OF UNP Q9U6Y8, AN ENGINEERED TR LINKER, AND RESIDUES 3-149 OF UNP P62161. UNP Q9U6Y8 RESIDUES Q66, Y67, AND G68 ARE FORMING THE CHROMOPHORE NRQ.

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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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 73mM malonic acid, 10mM ammonium citrate tribasic, 5mM succinic acid, 12mM malic acid, 16mM sodium acetate trihydrate, 20mM sodium formate, 6mM ammonium tartrate dibasic, 12% PEG 3350, pH 5, ...Details: 73mM malonic acid, 10mM ammonium citrate tribasic, 5mM succinic acid, 12mM malic acid, 16mM sodium acetate trihydrate, 20mM sodium formate, 6mM ammonium tartrate dibasic, 12% PEG 3350, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / 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: 2.2→54.77 Å / Num. all: 40865 / Num. obs: 40865 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.32 Å / % possible all: 100

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.6.0111refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H5Q, 3SG3

2h5q

3sg3


Resolution: 2.2→68.28 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.21 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25732 2049 5 %RANDOM
Rwork0.19344 ---
obs0.19659 38794 99.97 %-
all-40865 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-0.14 Å2
2--0.99 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.2→68.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6092 0 8 99 6199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0226221
X-RAY DIFFRACTIONr_bond_other_d0.0010.024340
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.9648371
X-RAY DIFFRACTIONr_angle_other_deg0.97310537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67724.734319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.51151109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4511539
X-RAY DIFFRACTIONr_chiral_restr0.1110.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216983
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021278
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 145 -
Rwork0.253 2783 -
obs--99.97 %

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