6Y75

BIL2 domain from T.thermophila BUBL1 locus (C1A-N143A)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis of ubiquitination mediated by protein splicing in early Eukarya.

Chiarini, V., Fiorillo, A., Camerini, S., Crescenzi, M., Nakamura, S., Battista, T., Guidoni, L., Colotti, G., Ilari, A.

(2021) Biochim Biophys Acta Gen Subj 1865: 129844-129844

  • DOI: https://doi.org/10.1016/j.bbagen.2021.129844
  • Primary Citation of Related Structures:  
    6TMM, 6Y75

  • PubMed Abstract: 

    Inteins are intervening proteins, which are known to perform protein splicing. The reaction results in the production of an intein domain and an inteinless protein, which shows no trace of the insertion. BIL2 is part of the polyubiquitin locus of Tetrahymena thermophila (BUBL), where two bacterial-intein-like (BIL) domains lacking the C + 1 nucleophile, are flanked by two independent ubiquitin-like domains (ubl4/ubl5).

    • Organizational Affiliation: 

    Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014 Helsinki, Finland.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)(+)--arginine ADP-ribosyltransferase
A, C
153Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00085190
EC: 2.4.2.31
UniProt
Find proteins for Q236S9 (Tetrahymena thermophila (strain SB210))
Explore Q236S9 
Go to UniProtKB:  Q236S9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ236S9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)(+)--arginine ADP-ribosyltransferase
B, D
150Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00085190
EC: 2.4.2.31
UniProt
Find proteins for Q236S9 (Tetrahymena thermophila (strain SB210))
Explore Q236S9 
Go to UniProtKB:  Q236S9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ236S9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
K [auth C],
L [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT
Query on FMT
Download Ideal Coordinates CCD File 
H [auth B],
J [auth B]		FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.821α = 90
b = 67.605β = 114.58
c = 82.445γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Italian Ministry of EducationItalyPRIN20154JRJPP

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description