7CKG

Crystal structure of TMSiPheRS complexed with TMSiPhe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.1 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
Tyrosine--tRNA ligase
A, B
314Methanocaldococcus jannaschii DSM 2661Mutation(s): 7 
Gene Names: tyrSMJ0389
EC: 6.1.1.1
UniProt
Find proteins for Q57834 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57834 
Go to UniProtKB:  Q57834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57834
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TSQ (Subject of Investigation/LOI)
Query on TSQ

Download Ideal Coordinates CCD File 
C [auth B]4-(trimethylsilyl)-L-phenylalanine
C12 H19 N O2 Si
YJYWOZDNAZTLQC-NSHDSACASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.102α = 90
b = 83.426β = 90
c = 106.235γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2021-03-31
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description