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- PDB-4ik9: High resolution structure of GCaMP3 dimer form 2 at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 4ik9
TitleHigh resolution structure of GCaMP3 dimer form 2 at pH 7.5
ComponentsRCaMP, Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / calcium indicator / mutants / fluorescent intensity / dimerization / beta-barrel / Calmodulin / Ca ion / Cytpplasm
Function / homology
Function and homology information


enzyme regulator activity / bioluminescence / generation of precursor metabolites and energy / calcium ion binding
Similarity search - Function
: / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...: / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / RCaMP / Green fluorescent protein
Similarity search - Component
Biological speciesEntacmaea quadricolor (sea anemone)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, Y. / Song, X. / Miao, L. / Zhu, Y. / Ji, G.
CitationJournal: Protein Cell / Year: 2013
Title: Structural insight into enhanced calcium indicator GCaMP3 and GCaMPJ to promote further improvement.
Authors: Chen, Y. / Song, X. / Ye, S. / Miao, L. / Zhu, Y. / Zhang, R.G. / Ji, G.
History
DepositionDec 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_distant_solvent_atoms / struct_ref_seq_dif
Item: _entity.pdbx_mutation / _struct_ref_seq_dif.align_id ..._entity.pdbx_mutation / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RCaMP, Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8116
Polymers50,5441
Non-polymers2665
Water8,377465
1
A: RCaMP, Green fluorescent protein
hetero molecules

A: RCaMP, Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,62212
Polymers101,0892
Non-polymers53310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8030 Å2
ΔGint-158 kcal/mol
Surface area35600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.617, 46.749, 68.753
Angle α, β, γ (deg.)90.00, 100.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RCaMP, Green fluorescent protein


Mass: 50544.391 Da / Num. of mol.: 1
Mutation: M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T
Source method: isolated from a genetically manipulated source
Details: CHIMERA OF 10 EXPRESSION TAGS, RESIDUES 1-48 OF RCaMP, LINKER LE, RESIDUES 149-238 OF GREEN FLUORESCENT PROTEIN, LINKER GGTGGSMV, RESIDUES 2-144 OF GREEN FLUORESCENT PROTEIN, RESIDUES 284-432 OF RCaMP
Source: (gene. exp.) Entacmaea quadricolor (sea anemone), (gene. exp.) Aequorea victoria (jellyfish)
Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: K4DIE3, UniProt: P42212
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence details(1) THIS CHIMERA COMPRISES OF 10 EXPRESSION TAGS, RESIDUES 1-48 OF RCaMP, LINKER LE, RESIDUES 149- ...(1) THIS CHIMERA COMPRISES OF 10 EXPRESSION TAGS, RESIDUES 1-48 OF RCaMP, LINKER LE, RESIDUES 149-238 OF GREEN FLUORESCENT PROTEIN, LINKER GGTGGSMV, RESIDUES 2-144 OF GREEN FLUORESCENT PROTEIN, RESIDUES 284-432 OF RCaMP (2) RESIDUE SER 222 HAS BEEN MUTATED TO GLY. RESIDUES GLY 222, TYR 223 AND GLY 224 CONSTITUTE THE CHROMOPHORE CRO 222

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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: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES pH 7.5, (NH4)2SO4, 21% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.4→26 Å / Num. obs: 76958 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.4→1.42 Å / % possible all: 95.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→26 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.252 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19497 1824 5.1 %RANDOM
Rwork0.15945 ---
obs0.16128 34197 98.1 %-
all-34859 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.283 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20.01 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 11 465 3609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193212
X-RAY DIFFRACTIONr_bond_other_d0.0060.023024
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.9684326
X-RAY DIFFRACTIONr_angle_other_deg0.9636992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0135396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74225.276163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49815582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2121517
X-RAY DIFFRACTIONr_chiral_restr0.1340.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023650
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02715
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 133 -
Rwork0.177 2547 -
obs--99.89 %

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