1IGN | pdb_00001ign

DNA-BINDING DOMAIN OF RAP1 IN COMPLEX WITH TELOMERIC DNA SITE

• PDB DOI: https://doi.org/10.2210/pdb1IGN/pdb
• NAKB: 1IGN

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


• Deposited: 1996-02-29 Released: 1997-01-27 
• Deposition Author(s): Koenig, P., Giraldo, R., Chapman, L., Rhodes, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.294 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA.

Konig, P., Giraldo, R., Chapman, L., Rhodes, D.

(1996) Cell 85: 125-136

• PubMed: 8620531 
• DOI: https://doi.org/10.1016/s0092-8674(00)81088-0
• Primary Citation Related Structures: 
  1IGN


• PubMed Abstract: 
  

  Telomeres, the nucleoprotein complexes at the ends of eukaryotic chromosomes, are essential for chromosome stability. In the yeast S. cerevisiae, telomeric DNA is bound in a sequence-specific manner by RAP1, a multifunctional protein also involved in transcriptional regulation. Here we report the crystal structure of the DNA-binding domain of RAP1 in complex with telomeric DNA site at 2.25 A resolution. The protein contains two similar domains that bind DNA in a tandem orientation, recognizing a tandemly repeated DNA sequence. The domains are structurally related to the homeodomain and the proto-oncogene Myb, but show novel features in their DNA-binding mode. A structured linker between the domains and a long C-terminal tail contribute to the binding specificity. This structure provides insight into the recognition of the conserved telomeric DNA sequences by a protein.

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Organizational Affiliation: 
• Medical Research Council, Laboratory of Molecular Biology, Cambridge, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 80.64 kDa 
• Atom Count: 4,908 
• Modeled Residue Count: 453 
• Deposited Residue Count: 568 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (RAP1)	E [auth A], F [auth B]	246	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: RAP1 DNA BINDING DOMAIN
UniProt
Find proteins for P11938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P11938  Go to UniProtKB:  P11938

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*CP*AP*CP*AP*CP*CP*CP*AP*CP*AP*CP*AP*CP*C P*AP*G)-3')	A [auth C], C [auth E]	19	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*TP*GP*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G P*CP*G)-3')	B [auth D], D [auth F]	19	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.294 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.61	α = 90
b = 90.61	β = 90
c = 80.36	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-01-27 
Deposition Author(s): Koenig, P., Giraldo, R., Chapman, L., Rhodes, D.

Revision History  

• Version 1.0: 1997-01-27
  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: 2017-06-28
  Changes: Database references
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references