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- PDB-4ik4: High resolution structure of GCaMP3 at pH 5.0 -

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Basic information

Entry
Database: PDB / ID: 4ik4
TitleHigh resolution structure of GCaMP3 at pH 5.0
ComponentsRCaMP, Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / calcium indicator / mutants / fluorescent intensity / dimerization / beta barrel / Calmodulin
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
RCaMP / Green fluorescent protein
Similarity search - Component
Biological speciesEntacmaea quadricolor (sea anemone)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 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 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: database_PDB_caveat / entity ...database_PDB_caveat / entity / entity_src_gen / 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 1.2Oct 30, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / 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

Downloads & links

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Assembly

Deposited unit
A: RCaMP, Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7055
Polymers50,5441
Non-polymers1604
Water4,720262
1
A: RCaMP, Green fluorescent protein
hetero molecules

A: RCaMP, Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,40910
Polymers101,0892
Non-polymers3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7910 Å2
ΔGint-154 kcal/mol
Surface area34740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.486, 46.917, 66.775
Angle α, β, γ (deg.)90.00, 100.53, 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 11-58 OF RCaMP, LINKER LE, RESIDUES 61-150 OF GREEN FLUORESCENT PROTEIN, LINKER GGTGGSMV, RESIDUES 159-299 OF GREEN FLUORESCENT PROTEIN, RESIDUES 300-448 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence details(1) THIS CHIMERA COMPRISES OF 10 EXPRESSION TAGS, RESIDUES 11-58 OF RCaMP, LINKER LE, RESIDUES 61- ...(1) THIS CHIMERA COMPRISES OF 10 EXPRESSION TAGS, RESIDUES 11-58 OF RCaMP, LINKER LE, RESIDUES 61-150 OF GREEN FLUORESCENT PROTEIN, LINKER GGTGGSMV, RESIDUES 159-299 OF GREEN FLUORESCENT PROTEIN, RESIDUES 300-448 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: 1.94 Å3/Da / Density % sol: 36.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Bis-Tris pH 5.0, (NH4)2SO4 and 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 22, 2012
RadiationMonochromator: Be filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→22.11 Å / Num. all: 26565 / Num. obs: 26008 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.05 Å / % possible all: 74.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→22.11 Å / SU ML: 0.25 / σ(F): 0.25 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 1318 5.08 %Random
Rwork0.1719 ---
all0.1851 26106 --
obs0.174 25958 99.43 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.688 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.286 Å20 Å20.8786 Å2
2---0.1928 Å20 Å2
3---0.4788 Å2
Refinement stepCycle: LAST / Resolution: 2.01→22.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 4 262 3420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.105
X-RAY DIFFRACTIONf_dihedral_angle_d17.71
X-RAY DIFFRACTIONf_chiral_restr0.087
X-RAY DIFFRACTIONf_plane_restr0.005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0104-2.09080.27531330.2133268198
2.0908-2.18590.2561580.17192700100
2.1859-2.3010.23171290.17352730100
2.301-2.4450.25371450.17732744100
2.445-2.63350.25191520.18312738100
2.6335-2.8980.25151510.18412723100
2.898-3.31620.21691470.1763274799
3.3162-4.17350.1791530.16092753100
4.1735-22.11130.18131500.1637282499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0205-0.03650.3451.93230.79651.20960.0005-0.15710.1899-0.1440.2314-0.2775-0.33790.5011-0.06670.21470.0023-0.00650.3080.00130.234541.139337.939144.6272
22.5611-1.26450.73371.99-1.11432.03470.1059-0.0161-0.1695-0.12610.03490.11660.1046-0.0118-0.12830.1894-0.0411-0.01370.1547-0.0030.175345.012526.806510.5172
31.57751.2094-0.5711.9189-0.45131.25590.0784-0.1510.04050.0945-0.06220.0577-0.13610.0628-0.01220.2197-0.0135-0.00110.28570.01460.190476.107734.355523.9217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 36:57)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 58:306)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 307:447)

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