1SKN | pdb_00001skn

THE BINDING DOMAIN OF SKN-1 IN COMPLEX WITH DNA: A NEW DNA-BINDING MOTIF

• PDB DOI: https://doi.org/10.2210/pdb1SKN/pdb
• NAKB: 1SKN

• Classification: TRANSCRIPTION/DNA
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-03-30 Released: 1998-06-24 
• Deposition Author(s): Rupert, P.B., Daughdrill, G.W., Bowerman, B., Matthews, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.337 (Depositor), 0.330 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

A new DNA-binding motif in the Skn-1 binding domain-DNA complex.

Rupert, P.B., Daughdrill, G.W., Bowerman, B., Matthews, B.W.

(1998) Nat Struct Biol 5: 484-491

• PubMed: 9628487 
• DOI: https://doi.org/10.1038/nsb0698-484
• Primary Citation of Related Structures:  
  1SKN


• PubMed Abstract: 
  

  The DNA-binding domain of Skn-1, a developmental transcription factor that specifies mesoderm in C. elegans, is shown by X-ray crystallography to have a novel fold in which a compact, monomeric, four-helix unit organizes two DNA-contact elements. At the C-terminus, a helix extends from the domain to occupy the major groove of DNA in a manner similar to bZip proteins. Skn-1, however, lacks the leucine zipper found in all bZips. Additional contacts with the DNA are made by a short basic segment at the N-terminus of the domain, reminiscent of the 'homeodomain arm'.

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Organizational Affiliation: 

Institute of Molecular Biology, Department of Chemistry, University of Oregon, Eugene 97403, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.4 kDa 
• Atom Count: 1,263 
• Modelled Residue Count: 104 
• Deposited Residue Count: 122 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-BINDING DOMAIN OF SKN-1	C [auth P]	92	Caenorhabditis elegans	Mutation(s): 0  Gene Names: SKN-1
UniProt
Find proteins for P34707 (Caenorhabditis elegans) Explore P34707  Go to UniProtKB:  P34707

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*TP*CP*CP*C)-3')	A	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*GP*GP*GP*AP*TP*GP*AP*CP*AP*TP*TP*GP*T)-3')	B	15	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LDA	D [auth P]	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.337 (Depositor), 0.330 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.13	α = 90
b = 93.39	β = 90
c = 53.45	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement
XTALVIEW	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-06-24 
Deposition Author(s): Rupert, P.B., Daughdrill, G.W., Bowerman, B., Matthews, B.W.

Revision History  

• Version 1.0: 1998-06-24
  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: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations