Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.66 kDa 
• Atom Count: 606 
• Modelled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1

5XK5

Relaxed state of S65-phosphorylated ubiquitin

• PDB DOI: 10.2210/pdb5XK5/pdb
• BMRB: 36082

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-05-05 Released: 2017-06-28 
• Deposition Author(s): Xu, D., Zhou, G., Qin, L.Y., Ran, M.L., Zhang, C.L., Liu, K., Liu, Z., Zhang, W.P., Tang, C.
• Funding Organization(s): the Chinese Ministry of Science and Technology, the 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

Ubiquitin S65 phosphorylation engenders a pH-sensitive conformational switch

Dong, X., Gong, Z., Lu, Y.B., Liu, K., Qin, L.Y., Ran, M.L., Zhang, C.L., Liu, Z., Zhang, W.P., Tang, C.

(2017) Proc Natl Acad Sci U S A 114: 6770-6775

• PubMed: 28611216 
• DOI: 10.1073/pnas.1705718114
• Primary Citation of Related Structures:  
  5XK4, 5XK5


• PubMed Abstract: 
  

Ubiquitin (Ub) is an important signaling protein. Recent studies have shown that Ub can be enzymatically phosphorylated at S65, and that the resulting pUb exhibits two conformational states-a relaxed state and a retracted state. However, crystallization efforts have yielded only the structure for the relaxed state, which was found similar to that of unmodified Ub. Here we present the solution structures of pUb in both states obtained through refinement against state-specific NMR restraints. We show that the retracted state differs from the relaxed state by the retraction of the last β-strand and by the extension of the second α-helix. Further, we show that at 7.2, the pK _a value for the phosphoryl group in the relaxed state is higher by 1.4 units than that in the retracted state. Consequently, pUb exists in equilibrium between protonated and deprotonated forms and between retracted and relaxed states, with protonated/relaxed species enriched at slightly acidic pH and deprotonated/retracted species enriched at slightly basic pH. The heterogeneity of pUb explains the inability of phosphomimetic mutants to fully mimic pUb. The pH-sensitive conformational switch is likely preserved for polyubiquitin, as single-molecule FRET data indicate that pH change leads to quaternary rearrangement of a phosphorylated K63-linked diubiquitin. Because cellular pH varies among compartments and changes upon pathophysiological insults, our finding suggests that pH and Ub phosphorylation confer additional target specificities and enable an additional layer of modulation for Ub signals.

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Organizational Affiliation: 

Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China.

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 160 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 5XK5 Olderado

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-05-05 
• Released Date: 2017-06-28 
Deposition Author(s): Xu, D., Zhou, G., Qin, L.Y., Ran, M.L., Zhang, C.L., Liu, K., Liu, Z., Zhang, W.P., Tang, C.

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Funding Organization	Location	Grant Number
the Chinese Ministry of Science and Technology	China	2013CB910200
the Chinese Ministry of Science and Technology	China	2016YFA0501200
the National Natural Science Foundation of China	China	31225007
the National Natural Science Foundation of China	China	31500595
the National Natural Science Foundation of China	China	31400735
the National Natural Science Foundation of China	China	31400644

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2017-07-12
  Changes: Database references