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 

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:  

  • 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 lanFP ...

    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

    Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico.,Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, IL 60439, USA.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation.,Synchrotron Radiation Research Section Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA.,Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico.,Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, IL 60439, USA. Electronic address: pletnevs@nih.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fluorescent protein lanFP6A
A, C
58Branchiostoma floridaeMutation(s): 0 
Find proteins for C3YRA1 (Branchiostoma floridae)
Go to UniProtKB:  C3YRA1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fluorescent protein lanFP6A
B, D
172Branchiostoma floridaeMutation(s): 0 
Find proteins for C3YRA1 (Branchiostoma floridae)
Go to UniProtKB:  C3YRA1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.133 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.726α = 90.00
b = 98.169β = 108.07
c = 55.145γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references
  • Version 1.2: 2019-12-04
    Type: Author supporting evidence