Primary Citation PubMed: 8703075
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A new way to rapidly create functional, fluorescent fusion proteins: random insertion of GFP with an in vitro transposition reaction.
(2002) BMC Neurosci 3
PubMed: 12086589 | PubMedCentral: PMC117241 | DOI: null
The GFP insertions into α s can be interpreted in the context of the structures of GFP (PDB file: 1EMA) and α s -GTPγ S (PDB file: 1AZT).
Publication Year: 2002
Molecular imaging in oncology.
(2004) Cancer Imaging 4
PubMed: 18250026 | PubMedCentral: PMC1434600 | DOI: 10.1102/1470-7330.2004.0060
Structure downloaded from Protein Data Bank (1EMA): http://www.rcsb.org/pdb/index.html .
Publication Year: 2004
Hue-shifted monomeric variants of Clavularia cyan fluorescent protein: identification of the molecular determinants of color and applications in fluorescence imaging.
(2008) BMC Biol 6
PubMed: 18325109 | PubMedCentral: PMC2292683 | DOI: 10.1186/1741-7007-6-13
(C) The chromophore environment of avGFP-S65T (and EGFP) showing the residues that structurally align with those represented in (A) (PDB code 1EMA) .
Publication Year: 2008
Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design.
(2009) J Biol Chem 284
PubMed: 19098007 | PubMedCentral: PMC2649101 | DOI: 10.1074/jbc.M807657200
Small-probe contact dot analysis ( 37 ) of the EGFP crystal structure (PDB 1EMA) shows that Val 163 is over-packed in the hydrophobic core, potentially clashing with Ile 152 .
Structural superimposition of the cpEGFP domain of either monomeric or dimeric GCaMP2 with the native GFP structures (PDB codes 1GFL ( 30 ) or 1EMA ( 31 )) shows root mean square deviations of only ∼0.4 Å when comparing all common 220 C α atoms (supplemental Fig.
The Ca 2+ -saturated dimer structure was solved as described previously ( 17 ) using the published coordinates of GFP (Protein Data Bank (PDB) entry 1EMA) and the coordinates of M13-bound calmodulin (PDB entry 1CDL) as search models.
Publication Year: 2009
The yeast nuclear pore complex and transport through it.
(2012) Genetics 190
PubMed: 22419078 | PubMedCentral: PMC3296253 | DOI: 10.1534/genetics.111.127803
(A) The extended NLS attached to a GFP reporter [green; PDB 1EMA ( Ormo et al. 1996 )] binds to a long region on the inside of the Kap60 superhelix [dark blue; PDB 1EE5 ( Liker et al. 2000 )], made of... alternating α-helical turns.
Publication Year: 2012
Computer modeling of the structure and spectra of fluorescent proteins.
(2009) Acta Naturae 1
PubMed: 22649601 | PubMedCentral: PMC3347511 | DOI: null
The first works [ 11 , 12 ] on molecular dynamical simulations with relatively short classical MD trajectories for the wild type and mutated variants of GFP were carried out using the heavy atom coord... nates of crystal structures 1EMA and 1EMB from the Protein Data Bank [ 13 ].
Structure of GFP (PDB ID: 1EMA).
Labeling amino acid residues corresponds to the structure PDB ID: 1EMA The known optical properties of GFP [ 14 ] exhibit two main absorption bands at 400 nm and 480 nm for the wild type of the protein.
Crystal structure of enhanced green fluorescent protein to 1.35 Å resolution reveals alternative conformations for Glu222.
(2012) PLoS One 7
PubMed: 23077555 | PubMedCentral: PMC3473056 | DOI: 10.1371/journal.pone.0047132
(B) Superposition of E222 sidechain conformer A (E222a; green) and B (E222b; yellow) with the E222 side chain from wt GFP (1GFL; grey) and S65T GFP (1EMA; cyan).
Whilst all of these waters superimpose with waters from the lower resolution EGFP structure 2Y0G, two of the waters (W 5 and W 6 ) are absent in both structures for wt GFP (1GFL) and for S65T GFP (1EMA).
Comparison of EGFP structures with wild-type GFP and S65T GFP structures Superpositioning of the structure obtained for EGFP with that of wt GFP (PDB entry 1GFL  ) and a S65T GFP mutant (PDB entry 1EMA  ) shows that the overall structures are very similar ( Figure 3A ); the RMSD over the backbone and all atoms of EGFP and wt GFP is 0.40 Å and 1.03 Å respectively, whilst the RMSD over backbone and all atoms of EGFP and S65T GFP are 0.29 Å and 0.85 Å, respectively.
Simplification of the genetic code: restricted diversity of genetically encoded amino acids.
(2012) Nucleic Acids Res 40
PubMed: 22909996 | PubMedCentral: PMC3488234 | DOI: 10.1093/nar/gks786
Structure determination and refinement The structures were determined by molecular replacement, using the GFP-S65T coordinate file (PDB code 1EMA) as a search model.
Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters.
(2013) J Mol Model 19
PubMed: 23187683 | PubMedCentral: PMC3536963 | DOI: 10.1007/s00894-012-1667-x
Table 13 Changes in Δ H f and RMS distortion upon going from PDB to PM7 structures for proteins Protein Change in Δ H f (kcal/mol) RMS distortion (Å) PDB Opt-10 Opt-3 Opt PDB O... t-10 Opt-3 Opt Chymotrypsin 1AFQ 2105.7 1083.8 898.2 0.0 0.000 0.055 0.109 1.264 Crambin 1CBN 605.4 402.7 343.6 0.0 0.000 0.115 0.172 0.985 Crambin (solvated) 1CBN 280.4 105.7 83.3 0.0 0.000 0.109 0.139 0.728 Green fluorescent protein 1EMA 2709.5 1121.8 969.4 0.0 0.000 0.067 0.126 0.966 Importin 1QGK 8944.2 4396.5 3011.1 0.0 0.000 0.060 0.116 1.300 Potassium channel 1JVM 3279.4 1507.4 1147.3 0.0 0.000 0.060 0.131 1.130 Using the starting structures, a complete PM7 unconstrained optimization was performed, resulting in an optimized structure (called “Opt”).
Publication Year: 2013
Enhanced yield of recombinant proteins with site-specifically incorporated unnatural amino acids using a cell-free expression system.
(2013) PLoS One 8
PubMed: 23844190 | PubMedCentral: PMC3699557 | DOI: 10.1371/journal.pone.0068363
Materials and Methods GFP Mutants The X-ray crystallographic structure of template GFP (PDB accession number: 1EMA), encoded by the GFP control vector (RTS, 5 PRIME, Hamburg, Germany), was analyzed to... choose sites for UAA incorporation.
Optogenetic control of ROS production.
(2014) Redox Biol 2
PubMed: 24563855 | PubMedCentral: PMC3926119 | DOI: 10.1016/j.redox.2014.01.019
Images of PDB IDs 1EMA  , 2WIQ  , 4EEP  were generated using PyMOL.
Publication Year: 2014
Mechanosignaling between central apparatus and radial spokes controls axonemal dynein activity.
(2014) J Cell Biol 204
PubMed: 24590175 | PubMedCentral: PMC3941055 | DOI: 10.1083/jcb.201312014
1EMA ) are shown for size comparison.
Abscisic acid dynamics in roots detected with genetically encoded FRET sensors.
(2014) Elife 3
PubMed: 24737862 | PubMedCentral: PMC3985517 | DOI: 10.7554/eLife.01741
The structure shown for dPAS110 is derived from a crystal structure of ABA bound to PYL1 and ABI1 (PDB: 3JRQ) ( Miyazono et al., 2009 ), and the structure shown for FRET donor enhanced dimer Cerulean ... edCerulean) and FRET acceptor enhanced dimer Citrine (edCitrine) are derived from a crystal structure of Aequorea victoria GFP (PDB:1EMA) ( Ormö et al., 1996 ).
PubMed ID is not available.
Published in 2014
The GPCR and CFP structures were prepared using PyMOL and the PDBs 3EML and 1EMA, respectively.
Gradated assembly of multiple proteins into supramolecular nanomaterials.
(2014) Nat Mater 13
PubMed: 24930032 | PubMedCentral: PMC4180598 | DOI: 10.1038/nmat3998
GFP adapted from PDB 1EMA in a. Figure 2 Fluorescent βTail fusion proteins stably integrate into Q11 nanofibers and microgels in smoothly gradated amounts, alone or in combination, without los... of activity a) Fluorescent βT fusion proteins integrated into Q11 nanofibers over the range of 0.25-1.5 μM in a βTail-dependent manner, as measured by loss of fluorescence from the supernatant.
Example structural models were obtained from PDB IDs 1EMA 52 ( Av ), 4HE4 53 ( Phi ), and 1GGX 54 ( Ds ); the Am CFP model is a Phyre server prediction 36 , 55 .
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