Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.51 kDa 
• Atom Count: 2273 
• Modelled Residue Count: 264 
• Deposited Residue Count: 264 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

2KM8

Interdomain RRM packing contributes to RNA recognition in the rna15, hrp1, anchor RNA 3' processing ternary complex

• PDB DOI: 10.2210/pdb2KM8/pdb
• BMRB: 16425
• NDB: 2KM8

• Classification: RNA binding protein/RNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-24 Released: 2010-07-28 
• Deposition Author(s): Leeper, T.C., Varani, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Novel Protein-Protein Contacts Facilitate mRNA 3'-Processing Signal Recognition by Rna15 and Hrp1.

Leeper, T.C., Qu, X., Lu, C., Moore, C., Varani, G.

(2010) J Mol Biol 401: 334-349

• PubMed: 20600122 
• DOI: 10.1016/j.jmb.2010.06.032
• Primary Citation of Related Structures:  
  2KM8


• PubMed Abstract: 
  

Precise 3'-end processing of mRNA is essential for correct gene expression, yet in yeast, 3'-processing signals consist of multiple ambiguous sequence elements. Two neighboring elements upstream of the cleavage site are particularly important for the accuracy (positioning element) and efficiency (efficiency element) of 3'-processing and are recognized by the RNA-binding proteins Rna15 and Hrp1, respectively. In vivo, these interactions are strengthened by the scaffolding protein Rna14 that stabilizes their association. The NMR structure of the 34 -kDa ternary complex of the RNA recognition motif (RRM) domains of Hrp1 and Rna15 bound to this pair of RNA elements was determined by residual dipolar coupling and paramagnetic relaxation experiments. It reveals how each of the proteins binds to RNA and introduces a novel class of protein-protein contact in regions of previously unknown function. These interdomain contacts had previously been overlooked in other multi-RRM structures, although a careful analysis suggests that they may be frequently present. Mutations in the regions of these contacts disrupt 3'-end processing, suggesting that they may structurally organize the ribonucleoprotein complexes responsible for RNA processing.

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Organizational Affiliation: 

Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA. [e-mail]

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA 3'-end-processing protein RNA15	B	84	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: 2.1, RNA15, YGL044C
UniProt
Find proteins for P25299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25299  Go to UniProtKB:  P25299

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear polyadenylated RNA-binding protein 4	C	167	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: HRP1, NAB4, NAB5, YOL123W
UniProt
Find proteins for Q99383 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q99383  Go to UniProtKB:  Q99383

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'	A	13	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2KM8 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-24 
• Released Date: 2010-07-28 
Deposition Author(s): Leeper, T.C., Varani, G.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-02-26
  Changes: Data collection, Database references, Derived calculations, Other