4EMQ

Crystal structure of a single mutant of Dronpa, the green-on-state PDM1-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the influence of a single mutation K145N on the oligomerization and photoswitching rate of Dronpa.

Nguyen Bich, N.Moeyaert, B.Van Hecke, K.Dedecker, P.Mizuno, H.Hofkens, J.Van Meervelt, L.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1653-1659

  • DOI: 10.1107/S0907444912039686
  • Primary Citation of Related Structures:  
    4EMQ

  • PubMed Abstract: 
  • The crystal structure of the on-state of PDM1-4, a single-mutation variant of the photochromic fluorescent protein Dronpa, is reported at 1.95 Å resolution. PDM1-4 is a Dronpa variant that possesses a slower off-switching rate than Dronpa and thus can effectively increase the image resolution in subdiffraction optical microscopy, although the precise molecular basis for this change has not been elucidated ...

    The crystal structure of the on-state of PDM1-4, a single-mutation variant of the photochromic fluorescent protein Dronpa, is reported at 1.95 Å resolution. PDM1-4 is a Dronpa variant that possesses a slower off-switching rate than Dronpa and thus can effectively increase the image resolution in subdiffraction optical microscopy, although the precise molecular basis for this change has not been elucidated. This work shows that the Lys145Asn mutation in PDM1-4 stabilizes the interface available for dimerization, facilitating oligomerization of the protein. No significant changes were observed in the chromophore environment of PDM1-4 compared with Dronpa, and the ensemble absorption and emission properties of PDM1-4 were highly similar to those of Dronpa. It is proposed that the slower off-switching rate in PDM1-4 is caused by a decrease in the potential flexibility of certain β-strands caused by oligomerization along the AC interface.


    Organizational Affiliation

    Biomolecular Architecture, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven (Heverlee), Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fluorescent protein Dronpa
A, B, C, D, E, F
A, B, C, D, E, F
255Echinophyllia sp. SC22Mutation(s): 2 
Gene Names: Dronpa
UniProt
Find proteins for Q5TLG6 (Echinophyllia sp. SC22)
Explore Q5TLG6 
Go to UniProtKB:  Q5TLG6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5TLG6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
N [auth D],
P [auth E],
G [auth A],
I [auth B],
K [auth C],
N [auth D],
P [auth E],
R [auth F]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
H [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
J [auth B],
L [auth C],
M [auth C],
O [auth D],
Q [auth E],
J [auth B],
L [auth C],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
T [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GYC
Query on GYC
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC14 H15 N3 O4 SCYS, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.539α = 90
b = 103.804β = 90
c = 177.255γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASESphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references