5HZT

Crystal structure of Dronpa-Cu2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structures of Dronpa complexed with quenchable metal ions provide insight into metal biosensor development

Kim, I.J.Kim, S.Park, J.Eom, I.Kim, S.Kim, J.H.Ha, S.C.Kim, Y.G.Hwang, K.Y.Nam, K.H.

(2016) FEBS Lett 590: 2982-2990

  • DOI: https://doi.org/10.1002/1873-3468.12316
  • Primary Citation of Related Structures:  
    5HZS, 5HZT, 5HZU

  • PubMed Abstract: 

    Many fluorescent proteins (FPs) show fluorescence quenching by specific metal ions, which can be applied towards metal biosensor development. In this study, we investigated the significant fluorescence quenching of Dronpa by Co(2+) and Cu(2+) ions. Crystal structures of Co(2+) -, Ni(2+) - and Cu(2+) -bound Dronpa revealed previously unseen, unique, metal-binding sites for fluorescence quenching. These metal ions commonly interact with surface-exposed histidine residues (His194-His210 and His210-His212), and interact indirectly with chromophores. Structural analysis of the Co(2+) - and Cu(2+) - binding sites of Dronpa provides insight into FP-based metal biosensor engineering.


  • Organizational Affiliation

    Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fluorescent protein Dronpa
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
215Echinophyllia sp. SC22Mutation(s): 1 
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
AA [auth H]
BA [auth H]
CA [auth I]
DA [auth I]
EA [auth J]
AA [auth H],
BA [auth H],
CA [auth I],
DA [auth I],
EA [auth J],
FA [auth J],
GA [auth K],
HA [auth K],
IA [auth L],
JA [auth L],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth C],
R [auth C],
S [auth D],
T [auth D],
U [auth E],
V [auth E],
W [auth F],
X [auth F],
Y [auth G],
Z [auth G]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
GYS
Query on GYS
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC14 H15 N3 O5SER, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.268α = 115.89
b = 105.961β = 107.68
c = 108.03γ = 94.12
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)Korea, Republic OfNRF-2014R1A1A2059440
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)Korea, Republic OfNRF-2014R1212513

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations