Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

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Protein Workshop | Ligand Explorer

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17128.57 
• Atom Count: 1160 
• Residue Count: 152 
• Unique protein chains: 2

5GO8

Linear tetra-ubiquitin

• DOI: 10.2210/pdb5GO8/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12


• Deposited: 2016-07-26 Released: 2016-11-02 
• Deposition Author(s): Gao, S., Pan, M., Zheng, Y.
• Funding Organization(s): National Basic Research Program of China 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.322 
• R-Value Work: 0.222 

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:  
  5GOK, 5GOJ, 5GOI, 5GOH, 5GOG, 5GOD, 5GOC, 5GOB, 5GO7


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ubiquitin	A	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
D-ubiquitin	B	76	Homo sapiens	Mutation(s): 0  Gene Names: UBA52 (UBCEP2)
Find proteins for P62987 (Homo sapiens) Go to Gene View: UBA52 Go to UniProtKB:  P62987

Small Molecules

Modified Residues  17 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DIL	B	D-PEPTIDE LINKING	C6 H13 N O2		--
DNE	B	D-PEPTIDE LINKING	C6 H13 N O2		--
DPR	B	D-PEPTIDE LINKING	C5 H9 N O2		--
DLY	B	D-PEPTIDE LINKING	C6 H14 N2 O2		--
DHI	B	D-PEPTIDE LINKING	C6 H10 N3 O2		--
DSN	B	D-PEPTIDE LINKING	C3 H7 N O3		--
DVA	B	D-PEPTIDE LINKING	C5 H11 N O2		--
DTH	B	D-PEPTIDE LINKING	C4 H9 N O3		--
DLE	B	D-PEPTIDE LINKING	C6 H13 N O2		--
DGL	B	D-PEPTIDE LINKING	C5 H9 N O4		--
DAL	B	D-PEPTIDE LINKING	C3 H7 N O2		--
DPN	B	D-PEPTIDE LINKING	C9 H11 N O2		--
DGN	B	D-PEPTIDE LINKING	C5 H10 N2 O3		--
DAS	B	D-PEPTIDE LINKING	C4 H7 N O4		--
DSG	B	D-PEPTIDE LINKING	C4 H8 N2 O3		--
DTY	B	D-PEPTIDE LINKING	C9 H11 N O3		--
DAR	B	D-PEPTIDE LINKING	C6 H15 N4 O2		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.322 
• R-Value Work: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 29.395	α = 90.00
b = 56.178	β = 91.44
c = 38.721	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Basic Research Program of China	China	2013CB932800

Revision History 

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