3AKO | pdb_00003ako

Crystal Structure of the Reassembled Venus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.229 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3AKO

This is version 2.0 of the entry. See complete history

Literature

Structure and characteristics of reassembled fluorescent protein, a new insight into the reassembly mechanisms

Isogai, M.Kawamoto, Y.Inahata, K.Fukada, H.Sugimoto, K.Tada, T.

(2011) Bioorg Med Chem Lett 21: 3021-3024

  • DOI: https://doi.org/10.1016/j.bmcl.2011.03.039
  • Primary Citation Related Structures: 
    3AKO

  • PubMed Abstract: 

    Bimolecular fluorescence complementation (BiFC) assay has been used widely to visualize protein-protein interactions in cells. However, there is a problem that fluorescent protein fragments have an ability to associate with each other independent of an interaction between proteins fused to the fragments. To facilitate the BiFC assay, we have attempted to determine the structure and characteristics of reassembled fluorescent protein, Venus. The anion-exchange chromatography showed an oligomer and a monomer of reassembled Venus. Our results suggested that the oligomer was formed by β-strands swapping without any serious steric clashes and was converted to the monomer. Crystal structure of reassembled Venus had an 11-stranded β-barrel fold, typical of GFP-derived fluorescent proteins. Based on the structural features, we have mutated to β-strand 7 and measured T(m) values. The results have revealed that the mutation influences the thermal stability of reassembled fluorescent complex.


  • Organizational Affiliation
    • Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.

Macromolecule Content 

  • Total Structure Weight: 122.66 kDa 
  • Atom Count: 8,022 
  • Modeled Residue Count: 902 
  • Deposited Residue Count: 1,064 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Venus
A, C, E, G
173Plant transformation vector pSITEII-4C1Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Venus
B, D, F, H
93Plant transformation vector pSITEII-4C1Mutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE8

Query on PE8



Download:Ideal Coordinates CCD File
J [auth E]3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CR2
Query on CR2
A, C, E, G
L-PEPTIDE LINKINGC13 H13 N3 O4GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.229 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.054α = 90
b = 116.046β = 90
c = 156.852γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection
  • Version 1.3: 2024-11-20
    Changes: Structure summary
  • Version 2.0: 2026-03-18
    Changes: Polymer sequence