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
  • Primary Citation of Related Structures:  
    5XBO

  • 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 sulfhyd ...

    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

    University of Chinese Academy of Sciences, Beijing, 100049, China. tanglab@wipm.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-B A76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UV excision repair protein RAD23 homolog A B49Homo sapiensMutation(s): 0 
Gene Names: RAD23A
Find proteins for P54725 (Homo sapiens)
Explore P54725 
Go to UniProtKB:  P54725
NIH Common Fund Data Resources
PHAROS:  P54725
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TB
Query on TB

Download Ideal Coordinates 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 
  • OLDERADO: 5XBO Olderado

Structure Validation

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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
    Changes: Author supporting evidence