5L2L | pdb_00005l2l

Nab2 Zn fingers 5-7 bound to A11G RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.152 (Depositor), 0.151 (DCC) 
  • R-Value Work: 
    0.131 (Depositor), 0.131 (DCC) 
  • R-Value Observed: 
    0.132 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5L2L

This is version 1.2 of the entry. See complete history

Literature

Structural basis for the dimerization of Nab2 generated by RNA binding provides insight into its contribution to both poly(A) tail length determination and transcript compaction in Saccharomyces cerevisiae.

Aibara, S.Gordon, J.M.Riesterer, A.S.McLaughlin, S.H.Stewart, M.

(2017) Nucleic Acids Res 45: 1529-1538

  • DOI: https://doi.org/10.1093/nar/gkw1224
  • Primary Citation Related Structures: 
    5L2L

  • PubMed Abstract: 

    In Saccharomyces cerevisiae generation of export-competent mRNPs terminates the nuclear phase of the gene expression pathway and facilitates transport to the cytoplasm for translation. Nab2 functions in this process to control both mRNP compaction that facilitates movement through nuclear pore complexes and the length of transcript poly(A) tails. Nab2 has a modular structure that includes seven CCCH Zn fingers that bind to A-rich RNAs and fingers 5–7 are critical for these functions. Here, we demonstrate, using both biophysical and structural methods, that binding A11G RNA induces dimerization of Zn fingers 5–7 mediated by the novel spatial arrangement of the fingers promoting each RNA chain binding two protein chains. The dimerization of Nab2 induced by RNA binding provides a basis for understanding its function in both poly(A) tail length regulation and in the compaction of mature transcripts to facilitate nuclear export.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK

Macromolecule Content 

  • Total Structure Weight: 52.44 kDa 
  • Atom Count: 4,031 
  • Modeled Residue Count: 334 
  • Deposited Residue Count: 356 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nab2p
A, B, E, F
77Saccharomyces cerevisiae YJM1574Mutation(s): 0 
Gene Names: NAB2H834_YJM1574G00138
UniProt
Find proteins for P32505 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32505 
Go to UniProtKB:  P32505
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32505
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*G)-3')
C, D, G, H
12Saccharomyces cerevisiae
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth E],
Q [auth E],
R [auth E],
S [auth F],
T [auth F],
U [auth F],
V [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.152 (Depositor), 0.151 (DCC) 
  • R-Value Work:  0.131 (Depositor), 0.131 (DCC) 
  • R-Value Observed: 0.132 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.669α = 90
b = 85.035β = 99.07
c = 64.956γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations