6ISU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.866 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1002/anie.201810814

  • 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 ...

    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.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing, 100081, China.,State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, the Graduate School at Shenzen, Tsinghua University, Shenzen, Guangdong, 518055, China.,Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase isozyme L3
A
230Homo sapiensMutation(s): 0 
Gene Names: UCHL3
EC: 3.4.19.12
Find proteins for P15374 (Homo sapiens)
Go to Gene View: UCHL3
Go to UniProtKB:  P15374
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
C
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SLZ
Query on SLZ
C
L-PEPTIDE LINKINGC5 H12 N2 O2 SLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.866 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 91.407α = 90.00
b = 94.204β = 90.00
c = 91.178γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21532004
National Natural Science Foundation of ChinaChina91753205
National Natural Science Foundation of ChinaChina31640016

Revision History 

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