6KOX | pdb_00006kox

Relaxed state of S65/T66 double-phosphorylated ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb6KOX/pdb

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


• Deposited: 2019-08-13 Released: 2019-08-28 
• Deposition Author(s): 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: 240 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Ubiquitin is double-phosphorylated by PINK1 for enhanced pH-sensitivity of conformational switch.

Ye, S.X., Gong, Z., Yang, J., An, Y.X., Liu, Z., Zhao, Q., Lescop, E., Dong, X., Tang, C.

(2019) Protein Cell 10: 908-913

• PubMed: 31278634 
• DOI: https://doi.org/10.1007/s13238-019-0644-x
• Primary Citation of Related Structures:  
  6KOW, 6KOX

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Organizational Affiliation: 
• Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
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, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071, China.
CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics of the Chinese Academy of Sciences, Dalian, 116023, China.
Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
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, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071, China. [e-mail].
Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China. [e-mail].
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, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 8.74 kDa 
• Atom Count: 610 
• Modeled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1

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 GTEx:  ENSG00000170315

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 240 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Dong, X., Tang, C.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2018YFA0507700
Ministry of Science and Technology (China)	China	2017YFA0505400
Ministry of Science and Technology (China)	China	2016YFA0501200
National Natural Science Foundation of China	China	91753132
National Natural Science Foundation of China	China	31770799

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Database references, Other
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary