5O9J

Crystal structure of transcription factor IIB Mja mini-intein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for the Persistence of Homing Endonucleases in Transcription Factor IIB Inteins.

Iwai, H.Mikula, K.M.Oeemig, J.S.Zhou, D.Li, M.Wlodawer, A.

(2017) J Mol Biol 429: 3942-3956

  • DOI: 10.1016/j.jmb.2017.10.016
  • Primary Citation of Related Structures:  
    5O9I, 5O9J

  • PubMed Abstract: 
  • Inteins are mobile genetic elements that are spliced out of proteins after translation. Some inteins contain a homing endonuclease (HEN) responsible for their propagation. Hedgehog/INTein (HINT) domains catalyzing protein splicing and their nested HEN domains are thought to be functionally independent because of the existence of functional mini-inteins without HEN domains ...

    Inteins are mobile genetic elements that are spliced out of proteins after translation. Some inteins contain a homing endonuclease (HEN) responsible for their propagation. Hedgehog/INTein (HINT) domains catalyzing protein splicing and their nested HEN domains are thought to be functionally independent because of the existence of functional mini-inteins without HEN domains. Despite the lack of obvious mutualism between HEN and HINT domains, HEN domains are persistently found at one specific site in inteins, indicating their potential functional role in protein splicing. Here we report crystal structures of inactive and active mini-inteins derived from inteins residing in the transcription factor IIB of Methanococcus jannaschii and Methanocaldococcus vulcanius, revealing a novel modified HINT fold that might provide new insights into the mutualism between the HEN and HINT domains. We propose an evolutionary model of inteins and a functional role of HEN domains in inteins.


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA. Electronic address: wlodawer@nih.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIB,Transcription initiation factor IIBA, B184Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: tfbMJ0782
EC: 3.1
UniProt
Find proteins for Q58192 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58192 
Go to UniProtKB:  Q58192
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58192
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
R [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
G [auth A],
H [auth A],
AA [auth B],
BA [auth B],
CA [auth B],
G [auth A],
H [auth A],
I [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
P [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
P [auth B],
Q [auth B]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

Download Ideal Coordinates CCD File 
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
J [auth A],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.36α = 77.42
b = 50.798β = 75.83
c = 60.118γ = 76.93
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MR-Rosettaphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland1131413
Academy of FinlandFinland137995
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesHHSN261200800001E

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2022-03-30
    Changes: Author supporting evidence, Database references