spacer
spacer

PDBsum entry 2emo
Go to PDB code: 
protein links
Luminescence PDB id
2emo

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
222 a.a. *
Waters ×61
* Residue conservation analysis
PDB id:
2emo
Name: Luminescence
Title: Green fluorescent protein from aequorea victoria, mutant
Structure: Green fluorescent protein. Chain: a. Synonym: gfp. Engineered: yes. Mutation: yes
Source: Aequorea victoria. Organism_taxid: 6100. Organ: photogenic organ. Tissue: circumoral ring canal. Gene: gfp. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.60Å     R-factor:   0.203     R-free:   0.343
Authors: G.Palm,A.Zdanov,A.Wlodawer
Key ref: G.J.Palm et al. (1997). The structural basis for spectral variations in green fluorescent protein. Nat Struct Biol, 4, 361-365. PubMed id: 9145105
Date:
31-Mar-97     Release date:   20-Aug-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P42212  (GFP_AEQVI) -  Green fluorescent protein from Aequorea victoria
Seq:
Struc: 		238 a.a.
222 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 

 
Nat Struct Biol 4:361-365 (1997)
PubMed id: 9145105  
 
 
The structural basis for spectral variations in green fluorescent protein.
G.J.Palm, A.Zdanov, G.A.Gaitanaris, R.Stauber, G.N.Pavlakis, A.Wlodawer.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21382348 A.A.Pakhomov, and V.I.Martynov (2011).
Probing the structural determinants of yellow fluorescence of a protein from Phialidium sp.
  Biochem Biophys Res Commun, 407, 230-235.  
21305683 M.Börsch, and J.Wrachtrup (2011).
Improving FRET-Based Monitoring of Single Chemomechanical Rotary Motors at Work.
  Chemphyschem, 12, 542-553.  
19067572 C.M.Megley, L.A.Dickson, S.L.Maddalo, G.J.Chandler, and M.Zimmer (2009).
Photophysics and dihedral freedom of the chromophore in yellow, blue, and green fluorescent protein.
  J Phys Chem B, 113, 302-308.  
19771337 J.J.van Thor (2009).
Photoreactions and dynamics of the green fluorescent protein.
  Chem Soc Rev, 38, 2935-2950.  
19783828 P.Gaytán, C.Contreras-Zambrano, M.Ortiz-Alvarado, A.Morales-Pablos, and J.Yáñez (2009).
TrimerDimer: an oligonucleotide-based saturation mutagenesis approach that removes redundant and stop codons.
  Nucleic Acids Res, 37, e125.  
19472338 S.Lindman, I.Johansson, E.Thulin, and S.Linse (2009).
Green fluorescence induced by EF-hand assembly in a split GFP system.
  Protein Sci, 18, 1221-1229.  
20016756 Y.Wang, and N.Wang (2009).
FRET and mechanobiology.
  Integr Biol (Camb), 1, 565-573.  
18676975 A.Tasdemir, F.Khan, T.A.Jowitt, L.Iuzzolino, S.Lohmer, S.Corazza, and T.J.Schmidt (2008).
Engineering of a monomeric fluorescent protein AsGFP499 and its applications in a dual translocation and transcription assay.
  Protein Eng Des Sel, 21, 613-622.  
18298671 D.Moes, A.Himmelbach, A.Korte, G.Haberer, and E.Grill (2008).
Nuclear localization of the mutant protein phosphatase abi1 is required for insensitivity towards ABA responses in Arabidopsis.
  Plant J, 54, 806-819.  
18574543 I.Muller, V.Sarramégna, M.Renault, V.Lafaquière, S.Sebai, A.Milon, and F.Talmont (2008).
The full-length mu-opioid receptor: a conformational study by circular dichroism in trifluoroethanol and membrane-mimetic environments.
  J Membr Biol, 223, 49-57.  
18305194 R.R.Chapleau, R.Blomberg, P.C.Ford, and M.Sagermann (2008).
Design of a highly specific and noninvasive biosensor suitable for real-time in vivo imaging of mercury (II) uptake.
  Protein Sci, 17, 614-622.
PDB codes: 2okw 2oky
18647110 Y.Wang, J.Y.Shyy, and S.Chien (2008).
Fluorescence proteins, live-cell imaging, and mechanobiology: seeing is believing.
  Annu Rev Biomed Eng, 10, 1.  
17434942 D.Arosio, G.Garau, F.Ricci, L.Marchetti, R.Bizzarri, R.Nifosì, and F.Beltram (2007).
Spectroscopic and structural study of proton and halide ion cooperative binding to gfp.
  Biophys J, 93, 232-244.
PDB codes: 2h6v 2o24 2o29 2o2b
18027983 X.Shi, J.Basran, H.E.Seward, W.Childs, C.R.Bagshaw, and S.G.Boxer (2007).
Anomalous negative fluorescence anisotropy in yellow fluorescent protein (YFP 10C): quantitative analysis of FRET in YFP dimers.
  Biochemistry, 46, 14403-14417.  
17965188 X.Shu, P.Leiderman, R.Gepshtein, N.R.Smith, K.Kallio, D.Huppert, and S.J.Remington (2007).
An alternative excited-state proton transfer pathway in green fluorescent protein variant S205V.
  Protein Sci, 16, 2703-2710.
PDB code: 2qle
17928700 Y.Arii, H.Yamaguchi, and S.Fukuoka (2007).
Production of a soluble recombinant prion protein fused to blue fluorescent protein without refolding or detergents in Escherichia coli cells.
  Biosci Biotechnol Biochem, 71, 2511-2514.  
16538631 G.Jung, and A.Zumbusch (2006).
Improving autofluorescent proteins: comparative studies of the effective brightness of Green Fluorescent Protein (GFP) mutants.
  Microsc Res Tech, 69, 175-185.  
16761088 J.J.van Thor, and J.T.Sage (2006).
Charge transfer in green fluorescent protein.
  Photochem Photobiol Sci, 5, 597-602.  
16771707 J.Wiedenmann, and G.U.Nienhaus (2006).
Live-cell imaging with EosFP and other photoactivatable marker proteins of the GFP family.
  Expert Rev Proteomics, 3, 361-374.  
16980366 K.Nienhaus, F.Renzi, B.Vallone, J.Wiedenmann, and G.U.Nienhaus (2006).
Chromophore-protein interactions in the anthozoan green fluorescent protein asFP499.
  Biophys J, 91, 4210-4220.
PDB code: 2c9i
16284263 P.Leiderman, D.Huppert, and N.Agmon (2006).
Transition in the temperature-dependence of GFP fluorescence: from proton wires to proton exit.
  Biophys J, 90, 1009-1018.  
17064887 S.J.Remington (2006).
Fluorescent proteins: maturation, photochemistry and photophysics.
  Curr Opin Struct Biol, 16, 714-721.  
16092146 D.Xie, and J.Zeng (2005).
Electronic excitations of green fluorescent proteins: protonation states of chromophore model compound in solutions.
  J Comput Chem, 26, 1487-1496.  
16153170 E.Larrainzar, F.O'Gara, and J.P.Morrissey (2005).
Applications of autofluorescent proteins for in situ studies in microbial ecology.
  Annu Rev Microbiol, 59, 257-277.  
15613627 G.Jung, J.Wiehler, and A.Zumbusch (2005).
The photophysics of green fluorescent protein: influence of the key amino acids at positions 65, 203, and 222.
  Biophys J, 88, 1932-1947.  
16033764 J.J.van Thor, G.Y.Georgiev, M.Towrie, and J.T.Sage (2005).
Ultrafast and low barrier motions in the photoreactions of the green fluorescent protein.
  J Biol Chem, 280, 33652-33659.
PDB codes: 1w7s 1w7t 1w7u
15681647 N.Agmon (2005).
Proton pathways in green fluorescence protein.
  Biophys J, 88, 2452-2461.  
15884066 S.Bonsma, R.Purchase, S.Jezowski, J.Gallus, F.Könz, and S.Völker (2005).
Green and red fluorescent proteins: photo- and thermally induced dynamics probed by site-selective spectroscopy and hole burning.
  Chemphyschem, 6, 838-849.  
15229884 E.S.Shih, and M.J.Hwang (2004).
Alternative alignments from comparison of protein structures.
  Proteins, 56, 519-527.  
14722062 G.T.Hanson, R.Aggeler, D.Oglesbee, M.Cannon, R.A.Capaldi, R.Y.Tsien, and S.J.Remington (2004).
Investigating mitochondrial redox potential with redox-sensitive green fluorescent protein indicators.
  J Biol Chem, 279, 13044-13053.
PDB codes: 1jc0 1jc1
15608070 J.T.Kennis, D.S.Larsen, I.H.van Stokkum, M.Vengris, J.J.van Thor, and R.van Grondelle (2004).
Uncovering the hidden ground state of green fluorescent protein.
  Proc Natl Acad Sci U S A, 101, 17988-17993.  
15111007 M.C.Ashby, K.Ibaraki, and J.M.Henley (2004).
It's green outside: tracking cell surface proteins with pH-sensitive GFP.
  Trends Neurosci, 27, 257-261.  
15584922 S.Bade, A.Rummel, C.Reisinger, T.Karnath, G.Ahnert-Hilger, H.Bigalke, and T.Binz (2004).
Botulinum neurotoxin type D enables cytosolic delivery of enzymatically active cargo proteins to neurones via unfolded translocation intermediates.
  J Neurochem, 91, 1461-1472.  
12944297 A.Follenius-Wund, M.Bourotte, M.Schmitt, F.Iyice, H.Lami, J.J.Bourguignon, J.Haiech, and C.Pigault (2003).
Fluorescent derivatives of the GFP chromophore give a new insight into the GFP fluorescence process.
  Biophys J, 85, 1839-1850.  
14613107 J.Wiehler, G.Jung, C.Seebacher, A.Zumbusch, and B.Steipe (2003).
Mutagenic stabilization of the photocycle intermediate of green fluorescent protein (GFP).
  Chembiochem, 4, 1164-1171.  
12466560 E.Ilegems, H.M.Pick, and H.Vogel (2002).
Monitoring mis-acylated tRNA suppression efficiency in mammalian cells via EGFP fluorescence recovery.
  Nucleic Acids Res, 30, e128.  
11967371 G.Chirico, F.Cannone, S.Beretta, A.Diaspro, B.Campanini, S.Bettati, R.Ruotolo, and A.Mozzarelli (2002).
Dynamics of green fluorescent protein mutant2 in solution, on spin-coated glasses, and encapsulated in wet silica gels.
  Protein Sci, 11, 1152-1161.  
12228718 G.H.Patterson, and J.Lippincott-Schwartz (2002).
A photoactivatable GFP for selective photolabeling of proteins and cells.
  Science, 297, 1873-1877.  
11740505 J.J.van Thor, T.Gensch, K.J.Hellingwerf, and L.N.Johnson (2002).
Phototransformation of green fluorescent protein with UV and visible light leads to decarboxylation of glutamate 222.
  Nat Struct Biol, 9, 37-41.
PDB code: 1hcj
11880630 M.A.Lill, and V.Helms (2002).
Proton shuttle in green fluorescent protein studied by dynamic simulations.
  Proc Natl Acad Sci U S A, 99, 2778-2781.  
11929996 Y.A.Labas, N.G.Gurskaya, Y.G.Yanushevich, A.F.Fradkov, K.A.Lukyanov, S.A.Lukyanov, and M.V.Matz (2002).
Diversity and evolution of the green fluorescent protein family.
  Proc Natl Acad Sci U S A, 99, 4256-4261.  
11209050 D.Yarbrough, R.M.Wachter, K.Kallio, M.V.Matz, and S.J.Remington (2001).
Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-A resolution.
  Proc Natl Acad Sci U S A, 98, 462-467.
PDB code: 1g7k
11459517 N.G.Gurskaya, A.P.Savitsky, Y.G.Yanushevich, S.A.Lukyanov, and K.A.Lukyanov (2001).
Color transitions in coral's fluorescent proteins by site-directed mutagenesis.
  BMC Biochem, 2, 6.  
10757992 A.F.Bell, X.He, R.M.Wachter, and P.J.Tonge (2000).
Probing the ground state structure of the green fluorescent protein chromophore using Raman spectroscopy.
  Biochemistry, 39, 4423-4431.  
10692343 A.Volkmer, V.Subramaniam, D.J.Birch, and T.M.Jovin (2000).
One- and two-photon excited fluorescence lifetimes and anisotropy decays of green fluorescent proteins.
  Biophys J, 78, 1589-1598.  
10590138 E.Olivetta, K.Pugliese, R.Bona, P.D'Aloja, F.Ferrantelli, A.C.Santarcangelo, G.Mattia, P.Verani, and M.Federico (2000).
cis expression of the F12 human immunodeficiency virus (HIV) Nef allele transforms the highly productive NL4-3 HIV type 1 to a replication-defective strain: involvement of both Env gp41 and CD4 intracytoplasmic tails.
  J Virol, 74, 483-492.  
  10673500 N.H.Chehab, A.Malikzay, M.Appel, and T.D.Halazonetis (2000).
Chk2/hCds1 functions as a DNA damage checkpoint in G(1) by stabilizing p53.
  Genes Dev, 14, 278-288.  
11056031 R.Battistutta, A.Negro, and G.Zanotti (2000).
Crystal structure and refolding properties of the mutant F99S/M153T/V163A of the green fluorescent protein.
  Proteins, 41, 429-437.
PDB code: 1b9c
10716703 T.M.Creemers, A.J.Lock, V.Subramaniam, T.M.Jovin, and S.Völker (2000).
Photophysics and optical switching in green fluorescent protein mutants.
  Proc Natl Acad Sci U S A, 97, 2974-2978.  
10882100 Y.I.Kim, R.E.Burton, B.M.Burton, R.T.Sauer, and T.A.Baker (2000).
Dynamics of substrate denaturation and translocation by the ClpXP degradation machine.
  Mol Cell, 5, 639-648.  
10359706 A.Sacchetti, V.Cappetti, C.Crescenzi, N.Celli, D.Rotilio, and S.Alberti (1999).
Red GFP and endogenous porphyrins.
  Curr Biol, 9, R391-R393.  
10512807 C.Scharnagl, R.Raupp-Kossmann, and S.F.Fischer (1999).
Molecular basis for pH sensitivity and proton transfer in green fluorescent protein: protonation and conformational substates from electrostatic calculations.
  Biophys J, 77, 1839-1857.  
10545381 E.B.Brown, E.S.Wu, W.Zipfel, and W.W.Webb (1999).
Measurement of molecular diffusion in solution by multiphoton fluorescence photobleaching recovery
  Biophys J, 77, 2837-2849.  
10339561 W.Weber, V.Helms, J.A.McCammon, and P.W.Langhoff (1999).
Shedding light on the dark and weakly fluorescent states of green fluorescent proteins.
  Proc Natl Acad Sci U S A, 96, 6177-6182.  
9671774 A.Valentin, W.Lu, M.Rosati, R.Schneider, J.Albert, A.Karlsson, and G.N.Pavlakis (1998).
Dual effect of interleukin 4 on HIV-1 expression: implications for viral phenotypic switch and disease progression.
  Proc Natl Acad Sci U S A, 95, 8886-8891.  
9836584 J.J.van Thor, A.J.Pierik, I.Nugteren-Roodzant, A.Xie, and K.J.Hellingwerf (1998).
Characterization of the photoconversion of green fluorescent protein with FTIR spectroscopy.
  Biochemistry, 37, 16915-16921.  
9512054 M.Kneen, J.Farinas, Y.Li, and A.S.Verkman (1998).
Green fluorescent protein as a noninvasive intracellular pH indicator.
  Biophys J, 74, 1591-1599.  
9665694 R.B.Robey, O.Ruiz, A.V.Santos, J.Ma, F.Kear, L.J.Wang, C.J.Li, A.A.Bernardo, and J.A.Arruda (1998).
pH-dependent fluorescence of a heterologously expressed Aequorea green fluorescent protein mutant: in situ spectral characteristics and applicability to intracellular pH estimation.
  Biochemistry, 37, 9894-9901.  
9782051 R.M.Wachter, M.A.Elsliger, K.Kallio, G.T.Hanson, and S.J.Remington (1998).
Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein.
  Structure, 6, 1267-1277.
PDB codes: 1yfp 2yfp
9759496 R.Y.Tsien (1998).
The green fluorescent protein.
  Annu Rev Biochem, 67, 509-544.  
9525926 T.T.Yang, P.Sinai, G.Green, P.A.Kitts, Y.T.Chen, L.Lybarger, R.Chervenak, G.H.Patterson, D.W.Piston, and S.R.Kain (1998).
Improved fluorescence and dual color detection with enhanced blue and green variants of the green fluorescent protein.
  J Biol Chem, 273, 8212-8216.  
9811841 U.Haupts, S.Maiti, P.Schwille, and W.W.Webb (1998).
Dynamics of fluorescence fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy.
  Proc Natl Acad Sci U S A, 95, 13573-13578.  
9434902 G.N.Phillips (1997).
Structure and dynamics of green fluorescent protein.
  Curr Opin Struct Biol, 7, 821-827.  
9384576 M.E.Greenberg, S.Bronson, M.Lock, M.Neumann, G.N.Pavlakis, and J.Skowronski (1997).
Co-localization of HIV-1 Nef with the AP-2 adaptor protein complex correlates with Nef-induced CD4 down-regulation.
  EMBO J, 16, 6964-6976.  
9245407 R.M.Wachter, B.A.King, R.Heim, K.Kallio, R.Y.Tsien, S.G.Boxer, and S.J.Remington (1997).
Crystal structure and photodynamic behavior of the blue emission variant Y66H/Y145F of green fluorescent protein.
  Biochemistry, 36, 9759-9765.
PDB code: 1bfp
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

spacer
spacer