5GO7 | pdb_00005go7

Linear tri-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.310 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1021/jacs.6b09545
  • Primary Citation 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.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin76Homo sapiensMutation(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
GTEx:  ENSG00000170315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
D-ubiquitin76Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
PHAROS:  P62987
GTEx:  ENSG00000221983 
Entity Groups  
UniProt GroupP62987
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  17 Unique
IDChains TypeFormula2D DiagramParent
DAL
Query on DAL
B
D-PEPTIDE LINKINGC3 H7 N O2

--

DAR
Query on DAR
B
D-PEPTIDE LINKINGC6 H15 N4 O2

--

DAS
Query on DAS
B
D-PEPTIDE LINKINGC4 H7 N O4

--

DGL
Query on DGL
B
D-PEPTIDE LINKINGC5 H9 N O4

--

DGN
Query on DGN
B
D-PEPTIDE LINKINGC5 H10 N2 O3

--

DHI
Query on DHI
B
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DIL
Query on DIL
B
D-PEPTIDE LINKINGC6 H13 N O2

--

DLE
Query on DLE
B
D-PEPTIDE LINKINGC6 H13 N O2

--

DLY
Query on DLY
B
D-PEPTIDE LINKINGC6 H14 N2 O2

--

DNE
Query on DNE
B
D-PEPTIDE LINKINGC6 H13 N O2

--

DPN
Query on DPN
B
D-PEPTIDE LINKINGC9 H11 N O2

--

DPR
Query on DPR
B
D-PEPTIDE LINKINGC5 H9 N O2

--

DSG
Query on DSG
B
D-PEPTIDE LINKINGC4 H8 N2 O3

--

DSN
Query on DSN
B
D-PEPTIDE LINKINGC3 H7 N O3

--

DTH
Query on DTH
B
D-PEPTIDE LINKINGC4 H9 N O3

--

DTY
Query on DTY
B
D-PEPTIDE LINKINGC9 H11 N O3

--

DVA
Query on DVA
B
D-PEPTIDE LINKINGC5 H11 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.310 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.955α = 71.54
b = 31.123β = 77.42
c = 32.18γ = 89.44
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection