6KRG

Crystal structure of sfGFP Y182TMSiPhe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DeSiphering receptor core-induced and ligand-dependent conformational changes in arrestin via genetic encoded trimethylsilyl 1 H-NMR probe.

Liu, Q.He, Q.T.Lyu, X.Yang, F.Zhu, Z.L.Xiao, P.Yang, Z.Zhang, F.Yang, Z.Y.Wang, X.Y.Sun, P.Wang, Q.W.Qu, C.X.Gong, Z.Lin, J.Y.Xu, Z.Song, S.L.Huang, S.M.Guo, S.C.Han, M.J.Zhu, K.K.Chen, X.Kahsai, A.W.Xiao, K.H.Kong, W.Li, F.H.Ruan, K.Li, Z.J.Yu, X.Niu, X.G.Jin, C.W.Wang, J.Sun, J.P.

(2020) Nat Commun 11: 4857-4857

  • DOI: https://doi.org/10.1038/s41467-020-18433-5
  • Primary Citation of Related Structures:  
    6KRG, 7CKG, 7CKH

  • PubMed Abstract: 

    Characterization of the dynamic conformational changes in membrane protein signaling complexes by nuclear magnetic resonance (NMR) spectroscopy remains challenging. Here we report the site-specific incorporation of 4-trimethylsilyl phenylalanine (TMSiPhe) into proteins, through genetic code expansion. Crystallographic analysis revealed structural changes that reshaped the TMSiPhe-specific amino-acyl tRNA synthetase active site to selectively accommodate the trimethylsilyl (TMSi) group. The unique up-field 1 H-NMR chemical shift and the highly efficient incorporation of TMSiPhe enabled the characterization of multiple conformational states of a phospho-β2 adrenergic receptor/β-arrestin-1(β-arr1) membrane protein signaling complex, using only 5 μM protein and 20 min of spectrum accumulation time. We further showed that extracellular ligands induced conformational changes located in the polar core or ERK interaction site of β-arr1 via direct receptor transmembrane core interactions. These observations provided direct delineation and key mechanism insights that multiple receptor ligands were able to induce distinct functionally relevant conformational changes of arrestin.


  • Organizational Affiliation

    Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein241Aequorea victoriaMutation(s): 7 
Gene Names: gfp
UniProt
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42212
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CRO
Query on CRO
A
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
TSQ
Query on TSQ
A
L-PEPTIDE LINKINGC12 H19 N O2 SiPHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.565α = 90
b = 68.565β = 90
c = 119.26γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description