Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.13 kDa 
• Atom Count: 1294 
• Modelled Residue Count: 147 
• Deposited Residue Count: 152 
• Unique protein chains: 2

5GO7

Linear tri-ubiquitin

• PDB DOI: 10.2210/pdb5GO7/pdb

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


• Deposited: 2016-07-26 Released: 2016-11-02 
• Deposition Author(s): Gao, S., Pan, M., Zheng, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.310 
• R-Value Work: 0.219 
• R-Value Observed: 0.225 

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

• PubMed: 27768314 
• DOI: 10.1021/jacs.6b09545
• Primary Citation of Related Structures:  
  5GO7, 5GO8, 5GOB, 5GOC, 5GOD, 5GOG, 5GOH, 5GOI, 5GOJ, 5GOK


• 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. 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	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
D-ubiquitin	B	76	Homo sapiens	Mutation(s): 0  Gene Names: UBA52, UBCEP2
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens) Explore P62987  Go to UniProtKB:  P62987
PHAROS:  P62987 GTEx:  ENSG00000221983

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.310 
• R-Value Work: 0.219 
• R-Value Observed: 0.225 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.955	α = 71.54
b = 31.123	β = 77.42
c = 32.18	γ = 89.44

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-07-26 
• Released Date: 2016-11-02 
Deposition Author(s): Gao, S., Pan, M., Zheng, Y.

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2016-11-16
  Changes: Database references
• Version 1.2: 2022-02-09
  Changes: Database references, Derived calculations