Biological Assembly 1  

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Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6131.56 
• Atom Count: 401 
• Residue Count: 19 
• Unique nucleic acid chains: 1

1KFO

CRYSTAL STRUCTURE OF AN RNA HELIX RECOGNIZED BY A ZINC-FINGER PROTEIN: AN 18 BASE PAIR DUPLEX AT 1.6 RESOLUTION

• DOI: 10.2210/pdb1KFO/pdb
• NDB: AR0039

• Classification: RNA


• Deposited: 2001-11-21 Released: 2001-12-07 
• Deposition Author(s): Lima, S., Hildenbrand, J., Korostelev, A., Hattman, S., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.288 
• R-Value Work: 0.260 

Literature

Crystal structure of an RNA helix recognized by a zinc-finger protein: an 18-bp duplex at 1.6 A resolution.

Lima, S., Hildenbrand, J., Korostelev, A., Hattman, S., Li, H.

(2002) RNA 8: 924-932

• PubMed: 12166647 


• PubMed Abstract: 
  

The crystal structure of the 19-mer RNA, 5'-GAAUGCCUGCGAGCAUCCC-3' has been determined from X-ray diffraction data to 1.6 A resolution by the multiwavelength anomalous diffraction method from crystals containing a brominated uridine. In the crystal, this RNA forms an 18-mer self-complementary double helix with the 19th nucleotide flipped out of the helix. This helix contains most of the target stem recognized by the bacteriophage Mu Com protein (control of mom), which activates translation of an unusual DNA modification enzyme, Mom. The 19-mer duplex, which contains one A.C mismatch and one A.C/G.U tandem wobble pair, was shown to bind to the Com protein by native gel electrophoresis shift assay. Comparison of the geometries and base stacking properties between Watson-Crick base pairs and the mismatches in the crystal structure suggest that both hydrogen bonding and base stacking are important for stabilizing these mismatched base pairs, and that the unusual geometry adopted by the A.C mismatch may reveal a unique structural motif required for the function of Com.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee 32306, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
5'-R(*GP*AP*AP*UP*GP*CP*CP*UP*GP*CP*GP*AP*GP*CP*AP*(5BU)P*CP*CP*C)-3'	A	19	N/A

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5BU	A	RNA LINKING	C9 H12 Br N2 O9 P		U

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.288 
• R-Value Work: 0.260 
• Space Group: P 6₃ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 45.336	α = 90.00
b = 45.336	β = 90.00
c = 95.129	γ = 120.00

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-21 
• Released Date: 2001-12-07 
• Deposition Author(s): Lima, S., Hildenbrand, J., Korostelev, A., Hattman, S., Li, H.

Revision History 

• Version 1.0: 2001-12-07
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance