2LHN | pdb_00002lhn

RNA-binding zinc finger protein

• PDB DOI: https://doi.org/10.2210/pdb2LHN/pdb
• BMRB: 17858

• Classification: NUCLEAR PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-12 Released: 2012-06-27 
• Deposition Author(s): Brockmann, C., Neuhaus, D., Stewart, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structural Basis for Polyadenosine-RNA Binding by Nab2 Zn Fingers and Its Function in mRNA Nuclear Export.

Brockmann, C., Soucek, S., Kuhlmann, S.I., Mills-Lujan, K., Kelly, S.M., Yang, J.C., Iglesias, N., Stutz, F., Corbett, A.H., Neuhaus, D., Stewart, M.

(2012) Structure 20: 1007-1018

• PubMed: 22560733 
• DOI: https://doi.org/10.1016/j.str.2012.03.011
• Primary Citation Related Structures: 
  2LHN


• PubMed Abstract: 
  

  Polyadenylation regulation and efficient nuclear export of mature mRNPs both require the polyadenosine-RNA-binding protein, Nab2, which contains seven CCCH Zn fingers. We describe here the solution structure of fingers 5-7, which are necessary and sufficient for high-affinity polyadenosine-RNA binding, and identify key residues involved. These Zn fingers form a single structural unit. Structural coherence is lost in the RNA-binding compromised Nab2-C437S mutant, which also suppresses the rat8-2 allele of RNA helicase Dbp5. Structure-guided Nab2 variants indicate that dbp5(rat8-2) suppression is more closely linked to hyperadenylation and suppression of mutant alleles of the nuclear RNA export adaptor, Yra1, than to affinity for polyadenosine-RNA. These results indicate that, in addition to modulating polyA tail length, Nab2 has an unanticipated function associated with generating export-competent mRNPs, and that changes within fingers 5-7 lead to suboptimal assembly of mRNP export complexes that are more easily disassembled by Dbp5 upon reaching the cytoplasm.

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Organizational Affiliation: 
• Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.42 kDa 
• Atom Count: 643 
• Modeled Residue Count: 80 
• Deposited Residue Count: 80 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear polyadenylated RNA-binding protein NAB2	A	80	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: NAB2, YGL122C
UniProt
Find proteins for P32505 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32505  Go to UniProtKB:  P32505

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Brockmann, C., Neuhaus, D., Stewart, M.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations