6M9Y

X-ray Structure of Branchiostoma floridae fluorescent protein lanFP6A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural Factors Enabling Successful GFP-Like Proteins with Alanine as the Third Chromophore-Forming Residue.

Muslinkina, L., Roldan-Salgado, A., Gaytan, P., Juarez-Gonzalez, V.R., Rudino, E., Pletneva, N., Pletnev, V., Dauter, Z., Pletnev, S.

(2019) J Mol Biol 431: 1397-1408

  • DOI: 10.1016/j.jmb.2019.02.013
  • Primary Citation of Related Structures:  
    6M9Z, 6M9Y, 6M9X, 6MAS

  • PubMed Abstract: 

    • GFP-like proteins from lancelets (lanFPs) is a new and least studied group that already generated several outstanding biomarkers (mNeonGreen is the brightest FP to date) and has some unique features. Here, we report the study of four homologous lanFPs wi ...

    GFP-like proteins from lancelets (lanFPs) is a new and least studied group that already generated several outstanding biomarkers (mNeonGreen is the brightest FP to date) and has some unique features. Here, we report the study of four homologous lanFPs with GYG and GYA chromophores. Until recently, it was accepted that the third chromophore-forming residue in GFP-like proteins should be glycine, and efforts to replace it were in vain. Now, we have the first structure of a fluorescent protein with a successfully matured chromophore that has alanine as the third chromophore-forming residue. Consideration of the protein structures revealed two alternative routes of posttranslational transformation, resulting in either chromophore maturation or hydrolysis of GYG/GYA tripeptide. Both transformations are catalyzed by the same set of catalytic residues, Arg88 and Glu35-Wat-Glu211 cluster, whereas the residues in positions 62 and 102 shift the equilibrium between chromophore maturation and hydrolysis.

    Organizational Affiliation: 

    Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, IL 60439, USA. Electronic address: pletnevs@nih.gov.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fluorescent protein lanFP6A A, C58Branchiostoma floridaeMutation(s): 0 
Gene Names: BRAFLDRAFT_75521
Find proteins for C3YRA1 (Branchiostoma floridae)
Explore C3YRA1 
Go to UniProtKB:  C3YRA1
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fluorescent protein lanFP6A B, D172Branchiostoma floridaeMutation(s): 0 
Gene Names: BRAFLDRAFT_75521
Find proteins for C3YRA1 (Branchiostoma floridae)
Explore C3YRA1 
Go to UniProtKB:  C3YRA1
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.726α = 90
b = 98.169β = 108.07
c = 55.145γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesHHSN261200800001E
Department of Energy (DOE, United States)United StatesW-31-109-Eng-38

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence