4WWU | pdb_00004wwu

Structure of Mex67:Mtr2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.284 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Domain organization within the nuclear export factor Mex67:Mtr2 generates an extended mRNA binding surface.

Aibara, S.Valkov, E.Lamers, M.Stewart, M.

(2015) Nucleic Acids Res 43: 1927-1936

  • DOI: https://doi.org/10.1093/nar/gkv030
  • Primary Citation Related Structures: 
    4WWU

  • PubMed Abstract: 

    The Mex67:Mtr2 complex is the principal yeast nuclear export factor for bulk mRNA and also contributes to ribosomal subunit export. Mex67 is a modular protein constructed from four domains (RRM, LRR, NTF2-like and UBA) that have been thought to be joined by flexible linkers like beads on a string, with the RRM and LRR domains binding RNAs and the NTF2-like and UBA domains binding FG-nucleoporins to facilitate movement through nuclear pores. Here, we show that the NTF2-like domain from Saccharomyces cerevisiae Mex67:Mtr2 also contributes to RNA binding. Moreover, the 3.3 Å resolution crystal structure of the Mex67(ΔUBA):Mtr2 complex, supplemented with small angle X-ray scattering data, indicated that the LRR domain has a defined spatial relationship to the Mex67(NTF2L):Mtr2 region. Conversely, the RRM domain and especially the UBA domain are more mobile. The conformation assumed by the LRR and NTF2-like domains results in clusters of positively-charged residues on each becoming arranged to form a continuous interface for binding RNA on the opposite side of the complex to the region that interacts with FG-nucleoporins to facilitate passage through nuclear pores.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.

Macromolecule Content 

  • Total Structure Weight: 526.42 kDa 
  • Atom Count: 18,797 
  • Modeled Residue Count: 2,349 
  • Deposited Residue Count: 4,640 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
mRNA export factor MEX67
A, B, D, E, G
A, B, D, E, G, H, J, K
488Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MEX67YPL169CP2520
UniProt
Find proteins for Q99257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99257 
Go to UniProtKB:  Q99257
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99257
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
mRNA transport regulator MTR2
C, F, I, L
184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR2YKL186C
UniProt
Find proteins for P34232 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34232 
Go to UniProtKB:  P34232
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34232
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
M [auth B]
N [auth B]
O [auth B]
P [auth C]
Q [auth E]
M [auth B],
N [auth B],
O [auth B],
P [auth C],
Q [auth E],
R [auth E],
S [auth F],
T [auth G],
U [auth H],
V [auth J],
W [auth K],
X [auth K]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.284 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.61α = 90
b = 76.72β = 94.09
c = 199.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations