5XBO

Lanthanoid tagging via an unnatural amino acid for protein structure characterization

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 160 
  • Conformers Submitted: 30 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Lanthanoid tagging via an unnatural amino acid for protein structure characterization

Jiang, W.X., Gu, X.H., Dong, X., Tang, C.

(2017) J. Biomol. NMR 67: 273-282

  • DOI: 10.1007/s10858-017-0106-9

  • PubMed Abstract: 

    • Lanthanoid pseudo-contact shift (PCS) provides long-range structural information between a paramagnetic tag and protein nuclei. However, for proteins with native cysteines, site-specific attachment may only utilize functional groups orthogonal to sul ...

    Lanthanoid pseudo-contact shift (PCS) provides long-range structural information between a paramagnetic tag and protein nuclei. However, for proteins with native cysteines, site-specific attachment may only utilize functional groups orthogonal to sulfhydryl chemistry. Here we report two lanthanoid probes, DTTA-C3-yne and DTTA-C4-yne, which can be conjugated to an unnatural amino acid pAzF in the target protein via azide-alkyne cycloaddition. Demonstrated with ubiquitin and cysteine-containing enzyme EIIB, we show that large PCSs of distinct profiles can be generated for each tag/lanthanoid combination. The DTTA-based lanthanoid tags are associated with large magnetic susceptibility tensors owing to the rigidity of the tags. In particular, introduction of the DTTA-C3 tag affords intermolecular PCSs and enables structural characterization of a transient protein complex between ubiquitin and a UBA domain. Together, we have expanded the repertoire of paramagnetic tags and the applicability of paramagnetic NMR.

    Organizational Affiliation: 

    CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071, Hubei, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
A
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UV excision repair protein RAD23 homolog A
B
49Homo sapiensMutation(s): 0 
Gene Names: RAD23A
Find proteins for P54725 (Homo sapiens)
Go to Gene View: RAD23A
Go to UniProtKB:  P54725
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TB
Query on TB
Download SDF File 
Download CCD File 
A
TERBIUM(III) ION
Tb
HKCRVXUAKWXBLE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 160 
  • Conformers Submitted: 30 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2013CB910200
Ministry of Science and Technology (China)China2016YFA0501200
National Natural Science Foundation of ChinaChina31225007
National Natural Science Foundation of ChinaChina31400644

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Author supporting evidence