7PRD

Solution structure of the chimeric Nrd1-Nab3 heterodimerization domains


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of Nrd1-Nab3 heterodimerization.

Chaves-Arquero, B.Martinez-Lumbreras, S.Camero, S.Santiveri, C.M.Mirassou, Y.Campos-Olivas, R.Jimenez, M.A.Calvo, O.Perez-Canadillas, J.M.

(2022) Life Sci Alliance 5

  • DOI: 10.26508/lsa.202101252
  • Primary Citation of Related Structures:  
    7PRD, 7PRE

  • PubMed Abstract: 
  • Heterodimerization of RNA binding proteins Nrd1 and Nab3 is essential to communicate the RNA recognition in the nascent transcript with the Nrd1 recognition of the Ser 5 -phosphorylated Rbp1 C-terminal domain in RNA polymerase II. The structure of a Nrd1-Nab3 chimera reveals the basis of heterodimerization, filling a missing gap in knowledge of this system ...

    Heterodimerization of RNA binding proteins Nrd1 and Nab3 is essential to communicate the RNA recognition in the nascent transcript with the Nrd1 recognition of the Ser 5 -phosphorylated Rbp1 C-terminal domain in RNA polymerase II. The structure of a Nrd1-Nab3 chimera reveals the basis of heterodimerization, filling a missing gap in knowledge of this system. The free form of the Nrd1 interaction domain of Nab3 (NRID) forms a multi-state three-helix bundle that is clamped in a single conformation upon complex formation with the Nab3 interaction domain of Nrd1 (NAID). The latter domain forms two long helices that wrap around NRID, resulting in an extensive protein-protein interface that would explain the highly favorable free energy of heterodimerization. Mutagenesis of some conserved hydrophobic residues involved in the heterodimerization leads to temperature-sensitive phenotypes, revealing the importance of this interaction in yeast cell fitness. The Nrd1-Nab3 structure resembles the previously reported Rna14/Rna15 heterodimer structure, which is part of the poly(A)-dependent termination pathway, suggesting that both machineries use similar structural solutions despite they share little sequence homology and are potentially evolutionary divergent.


    Organizational Affiliation

    Departamento de Química-Física Biológica, Instituto de Química-Física "Rocasolano" (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain jmperez@iqfr.csic.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein NRD1,HLJ1_G0022400.mRNA.1.CDS.1A125Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SCNYR20_0008007600SCP684_0008007200PACBIOSEQ_LOCUS5883
UniProt
Find proteins for P53617 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53617 
Go to UniProtKB:  P53617
Find proteins for P38996 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38996 
Go to UniProtKB:  P38996
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP53617P38996
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Autonomous Community of MadridSpainBMD-3770

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-01-26
    Changes: Database references