1TC3 | pdb_00001tc3

TRANSPOSASE TC3A1-65 FROM CAENORHABDITIS ELEGANS

• PDB DOI: https://doi.org/10.2210/pdb1TC3/pdb
• NAKB: 1TC3

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-07-07 Released: 1997-11-21 
• Deposition Author(s): Van Pouderoyen, G., Ketting, R.F., Perrakis, A., Plasterk, R.H.A., Sixma, T.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.318 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.227 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA.

van Pouderoyen, G., Ketting, R.F., Perrakis, A., Plasterk, R.H., Sixma, T.K.

(1997) EMBO J 16: 6044-6054

• PubMed: 9312061 
• DOI: https://doi.org/10.1093/emboj/16.19.6044
• Primary Citation Related Structures: 
  1TC3


• PubMed Abstract: 
  

  The crystal structure of the complex between the N-terminal DNA-binding domain of Tc3 transposase and an oligomer of transposon DNA has been determined. The specific DNA-binding domain contains three alpha-helices, of which two form a helix-turn-helix (HTH) motif. The recognition of transposon DNA by the transposase is mediated through base-specific contacts and complementarity between protein and sequence-dependent deformations of the DNA. The HTH motif makes four base-specific contacts with the major groove, and the N-terminus makes three base-specific contacts with the minor groove. The DNA oligomer adopts a non-linear B-DNA conformation, made possible by a stretch of seven G:C base pairs at one end and a TATA sequence towards the other end. Extensive contacts (seven salt bridges and 16 hydrogen bonds) of the protein with the DNA backbone allow the protein to probe and recognize the sequence-dependent DNA deformation. The DNA-binding domain forms a dimer in the crystals. Each monomer binds a separate transposon end, implying that the dimer plays a role in synapsis, necessary for the simultaneous cleavage of both transposon termini.

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Organizational Affiliation: 
• Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.39 kDa 
• Atom Count: 1,287 
• Modeled Residue Count: 92 
• Deposited Residue Count: 92 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TC3 TRANSPOSASE)	C	51	Caenorhabditis elegans	Mutation(s): 0  Gene Names: TC3A
UniProt
Find proteins for P34257 (Caenorhabditis elegans) Explore P34257  Go to UniProtKB:  P34257

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*GP*TP*CP*CP*TP*AP*TP*AP*GP*A P*AP*CP*TP*T)-3')	A	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*TP*TP*CP*TP*AP*TP*AP*GP*GP*AP*CP*CP*CP*CP*C P*CP*CP*T)-3')	B	20	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.318 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.227 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.18	α = 90
b = 202.79	β = 90
c = 62.14	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
TNT	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-11-21 
Deposition Author(s): Van Pouderoyen, G., Ketting, R.F., Perrakis, A., Plasterk, R.H.A., Sixma, T.K.

Revision History  

• Version 1.0: 1997-11-21
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references