5GOK

K11/K63-branched tri-Ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Monomer/Oligomer Quasi-Racemic Protein Crystallography

Gao, S.Pan, M.Zheng, Y.Huang, Y.Zheng, Q.Sun, D.Lu, L.Tan, X.Tan, X.Lan, H.Wang, J.Wang, T.Wang, J.Liu, L.

(2016) J Am Chem Soc 138: 14497-14502

  • DOI: 10.1021/jacs.6b09545
  • Primary Citation of Related Structures:  
    5GO8, 5GO7, 5GOH, 5GOG, 5GOJ, 5GOI, 5GOK, 5GOB, 5GOD, 5GOC

  • PubMed Abstract: 
  • Racemic or quasi-racemic crystallography recently emerges as a useful technology for solution of the crystal structures of biomacromolecules. It remains unclear to what extent the biomacromolecules of opposite handedness can differ from each other in ...

    Racemic or quasi-racemic crystallography recently emerges as a useful technology for solution of the crystal structures of biomacromolecules. It remains unclear to what extent the biomacromolecules of opposite handedness can differ from each other in racemic or quasi-racemic crystallography. Here we report a finding that monomeric d-ubiquitin (Ub) has propensity to cocrystallize with different dimers, trimers, and even a tetramer of l-Ub. In these cocrystals the unconnected monomeric d-Ubs can self-assemble to form pseudomirror images of different oligomers of l-Ub. This monomer/oligomer cocrystallization phenomenon expands the concept of racemic crystallography. Using the monomer/oligomer cocrystallization technology we obtained, for the first time the X-ray structures of linear M1-linked tri- and tetra-Ubs and a K11/K63-branched tri-Ub.


    Organizational Affiliation

    Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinA76Homo 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
D-ubiquitinB76Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
NIH Common Fund Data Resources
PHAROS  P62987
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.073α = 90
b = 52.911β = 90
c = 58.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of ChinaChina2013CB932800

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references