Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 43.38 kDa 
• Atom Count: 3314 
• Residue Count: 379 
• Unique protein chains: 3

6ISU

Crystal structure of Lys27-linked di-ubiquitin in complex with its selective interacting protein UCHL3

• DOI: 10.2210/pdb6ISU/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-19 Released: 2019-02-06 
• Deposition Author(s): Ding, S., Pan, M., Zheng, Q., Ren, Y., Hong, D.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.264 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

Literature

Chemical Protein Synthesis Enabled Mechanistic Studies on the Molecular Recognition of K27-linked Ubiquitin Chains.

Pan, M., Zheng, Q., Ding, S., Zhang, L., Qu, Q., Wang, T., Hong, D., Ren, Y., Liang, L., Chen, C., Mei, Z., Liu, L.

(2019) Angew Chem Int Ed Engl 58: 2627-2631

• PubMed: 30589182 
• DOI: 10.1002/anie.201810814
• Primary Citation of Related Structures:  
  6ISU


• PubMed Abstract: 
  

New synthetic strategies that exploited the strengths of both chemoselective ligation and recombinant protein expression were developed to prepare K27 di-ubiquitins (diUb), which enabled mechanistic studies on the molecular recognition of K27-linked Ubs by single-molecule Förster resonance energy transfer (smFRET) and X-ray crystallography. The results revealed that free K27 diUb adopted a compact conformation, whereas upon binding to UCHL3, K27 diUb was remodeled to an open conformation. The K27 isopeptide bond remained rigidly buried inside the diUb moiety during binding, an interesting unique structural feature that may explain the distinctive biological function of K27 Ub chains.

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Organizational Affiliation: 

State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, the Graduate School at Shenzen, Tsinghua University, Shenzen, Guangdong, 518055, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase isozyme L3	A	230	Homo sapiens	Mutation(s): 0  Gene Names: UCHL3 EC: 3.4.19.12
Find proteins for P15374 (Homo sapiens) Explore P15374  Go to UniProtKB:  P15374
NIH Common Fund Data Resources
PHAROS:  P15374 GTEx:  ENSG00000118939

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	C	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SLZ	C	L-PEPTIDE LINKING	C5 H12 N2 O2 S		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.264 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.407	α = 90
b = 94.204	β = 90
c = 91.178	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-11-19 
• Released Date: 2019-02-06 
Deposition Author(s): Ding, S., Pan, M., Zheng, Q., Ren, Y., Hong, D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	21532004
National Natural Science Foundation of China	China	91753205
National Natural Science Foundation of China	China	31640016

Revision History 

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Database references