Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.23 kDa 
• Atom Count: 987 
• Modelled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 2

5XBO

Lanthanoid tagging via an unnatural amino acid for protein structure characterization

• PDB DOI: 10.2210/pdb5XBO/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-21 Released: 2017-05-31 
• Deposition Author(s): Jiang, W., Gu, X., Dong, X., Tang, C.
• Funding Organization(s): Ministry of Science and Technology (China), National Natural Science Foundation of China

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Experimental Data Snapshot

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

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

• PubMed: 28365903 
• 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 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.

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Organizational Affiliation: 

University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	A	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UV excision repair protein RAD23 homolog A	B	49	Homo sapiens	Mutation(s): 0  Gene Names: RAD23A
UniProt & NIH Common Fund Data Resources
Find proteins for P54725 (Homo sapiens) Explore P54725  Go to UniProtKB:  P54725
PHAROS:  P54725 GTEx:  ENSG00000179262

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TB	C [auth A]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N

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

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-03-21 
• Released Date: 2017-05-31 
Deposition Author(s): Jiang, W., Gu, X., Dong, X., Tang, C.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2013CB910200
Ministry of Science and Technology (China)	China	2016YFA0501200
National Natural Science Foundation of China	China	31225007
National Natural Science Foundation of China	China	31400644

Revision History  

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