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: 10.25 kDa 
• Atom Count: 690 
• Modelled Residue Count: 46 
• Deposited Residue Count: 46 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1NYB

SOLUTION STRUCTURE OF THE BACTERIOPHAGE PHI21 N PEPTIDE-BOXB RNA COMPLEX

• PDB DOI: 10.2210/pdb1NYB/pdb
• NDB: 1NYB

• Classification: TRANSCRIPTION/RNA
• Organism(s): Enterobacteria phage phi21
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-02-12 Released: 2003-06-24 
• Deposition Author(s): Cilley, C.D., Williamson, J.R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Literature

Structural mimicry in the phage phi21 N peptide-boxB RNA complex

Cilley, C.D., Williamson, J.R.

(2003) RNA 9: 663-676

• PubMed: 12756325 
• DOI: 10.1261/rna.2189203
• Primary Citation of Related Structures:  
  1NYB


• PubMed Abstract: 
  

We determined the solution structure of a 22-amino-acid peptide from the amino-terminal domain of the bacteriophage phi21 N protein in complex with its cognate 24-mer boxB RNA hairpin using heteronuclear magnetic resonance spectroscopy. The N peptide binds as an alpha-helix and interacts predominately with the major groove side of the 5' half of the boxB RNA stem-loop. This binding interface is defined by surface complementarity of polar and nonpolar interactions, and little sequence-specific recognition. The phi21 boxB loop (CUAACC) has hydrogen bond and backbone torsions typical of the "U-turn" motif, as well as base stacking of the last 4 nt, and a hydrogen bonded C:C pair closing the loop. The exposed face of the phi21 boxB loop, in complex with the N peptide, is strikingly similar to the GNRA tetraloop-like folds of the related lambda and P22 bacteriophage N peptide-boxB RNA complexes. The N peptide-boxB complexes of the various phage, while individually distinct, provide similar structural features for interactions with the Escherichia coli host factors to enable antitermination.

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Organizational Affiliation: 

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable regulatory protein N	B [auth A]	22	Enterobacteria phage phi21	Mutation(s): 0  Gene Names: N
UniProt
Find proteins for P07243 (Enterobacteria phage phi21) Explore P07243  Go to UniProtKB:  P07243

Entity ID: 1
Molecule	Chains	Length	Organism	Image
BoxB RNA	A [auth B]	24	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1NYB Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-12 
• Released Date: 2003-06-24 
Deposition Author(s): Cilley, C.D., Williamson, J.R.

Revision History  

• Version 1.0: 2003-06-24
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2022-02-23
  Changes: Atomic model, Data collection, Database references, Derived calculations