Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.09 kDa 
• Atom Count: 1210 
• Modelled Residue Count: 144 
• Deposited Residue Count: 144 
• Unique protein chains: 1

1IUF

LOW RESOLUTION SOLUTION STRUCTURE OF THE TWO DNA-BINDING DOMAINS IN Schizosaccharomyces pombe ABP1 PROTEIN

• PDB DOI: 10.2210/pdb1IUF/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-03-04 Released: 2002-06-05 
• Deposition Author(s): Kikuchi, J., Iwahara, J., Kigawa, T., Murakami, Y., Okazaki, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 1 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure determination of the two DNA-binding domains in the Schizosaccharomyces pombe Abp1 protein by a combination of dipolar coupling and diffusion anisotropy restraints.

Kikuchi, J., Iwahara, J., Kigawa, T., Murakami, Y., Okazaki, T., Yokoyama, S.

(2002) J Biomol NMR 22: 333-347

• PubMed: 12018481 
• DOI: 10.1023/a:1014977808170
• Primary Citation of Related Structures:  
  1IUF


• PubMed Abstract: 
  

We have solved the solution structure of the N-terminal region of the fission yeast centromere protein, Abp1, bound to a 21-base pair DNA fragment bearing its recognition site (Mw = 30 kDa). Although the two DNA-binding domains in the Abpl protein were defined well by a conventional NOE-based NMR methodology, the overall structure of the Abpl protein was poorly defined, due to the lack of interdomain distance restraints. Therefore, we additionally used residual dipolar couplings measured in a weakly aligned state, and rotational diffusion anisotropies. Neither the NH residual dipolar couplings nor the backbone 15N T1/T2 data were sufficient to determine the overall structure of the Abpl protein, due to spectral overlap. We used a combination of these two orientational restraints (residual dipolar coupling and rotational diffusion anisotropy), which significantly improved the convergence of the overall structures. The range of the observed T1/T2 ratios was wider (20-50 for the secondary structure regions of Abp 1) than the previously reported data for several globular proteins, indicating that the overall shape of the Abp1.DNA complex is ellipsoid. This extended form would facilitate the recognition of the two separate sites in the relatively long DNA sequence by the DNA-binding domains of Apb1.

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Organizational Affiliation: 

RIKEN Genomic Sciences Center, Tsurumi, Yokohama, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
centromere abp1 protein	A	144	Schizosaccharomyces pombe	Mutation(s): 0
UniProt
Find proteins for P49777 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P49777  Go to UniProtKB:  P49777

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 1 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1IUF Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-04 
• Released Date: 2002-06-05 
Deposition Author(s): Kikuchi, J., Iwahara, J., Kigawa, T., Murakami, Y., Okazaki, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2002-06-05
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Database references, Derived calculations