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PDBsum entry 1oai

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Nuclear transport PDB id
1oai
Jmol
Contents
Protein chain
59 a.a. *
Ligands
ASP-SER-GLY-PHE-
SER-PHE-GLY-SER-
LYS
Waters ×127
* Residue conservation analysis
PDB id:
1oai
Name: Nuclear transport
Title: Complex between tap uba domain and fxfg nucleoporin peptide
Structure: Nuclear RNA export factor. Chain: a. Fragment: uba domain, residues 561-619. Synonym: tap, tip associating protein, mRNA export factor tap. Engineered: yes. Fxfg nucleoporin peptide. Chain: b. Fragment: nucleoporin peptide, residues 10-18.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
1.0Å     R-factor:   0.149     R-free:   0.159
Authors: R.P.Grant,D.Neuhaus,M.Stewart
Key ref:
R.P.Grant et al. (2003). Structural basis for the interaction between the Tap/NXF1 UBA domain and FG nucleoporins at 1A resolution. J Mol Biol, 326, 849-858. PubMed id: 12581645 DOI: 10.1016/S0022-2836(02)01474-2
Date:
14-Jan-03     Release date:   20-Feb-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9UBU9  (NXF1_HUMAN) -  Nuclear RNA export factor 1
Seq:
Struc:
 
Seq:
Struc:
619 a.a.
59 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     mRNA transport   1 term 

 

 
DOI no: 10.1016/S0022-2836(02)01474-2 J Mol Biol 326:849-858 (2003)
PubMed id: 12581645  
 
 
Structural basis for the interaction between the Tap/NXF1 UBA domain and FG nucleoporins at 1A resolution.
R.P.Grant, D.Neuhaus, M.Stewart.
 
  ABSTRACT  
 
The mRNA nuclear export function of Tap/NXF1 requires interactions with nuclear pore proteins (nucleoporins) that contain characteristic Phe-Gly repeats based on FG, GLFG or FxFG cores separated by hydrophilic linkers. FG-nucleoporins bind the two most C-terminal domains of Tap, which have NTF2 and UBA folds, respectively. We used a combination of NMR and X-ray crystallography to define the interaction interface between Tap UBA and FxFG nucleoporins and show that it involves primarily the two aromatic rings of the FxFG core that bind in a hydrophobic surface depression centred on Tap Cys588. NMR evidence indicates that the same depression mediates the binding of GLFG nucleoporins, which we confirmed by demonstrating competition between the two classes of repeat for binding to Tap UBA. Moreover, modification of Cys588 reduced the binding of Tap UBA to both GLFG and FxFG nucleoporins as well as to nuclear envelopes. These data underscore the central role of the conserved FG-nucleoporin repeat cores in binding to Tap UBA and indicate that functional differences between different classes of nucleoporins depend more on their spatial distribution in nuclear pores than on their binding to different sites on Tap UBA.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. (a) Stereo view of a space-filling model of the Tap UBA crystal structure, centred on the binding interface. Residues lining the hydrophobic pocket are in yellow and the FxFG-peptide is shown in black (b) Stereo model of the Tap UBA FG-binding pocket showing Tap residues (yellow) that make hydrophobic contacts with the FxFG peptide (black). Orientation as in (a).
Figure 4.
Figure 4. Contacts between the FxFG core peptide and Tap UBA observed in the crystal structure of their complex. The FxFG binding site on Tap UBA is defined by the side-chains of Met580, Trp584, Lys587, Cys588, Ala602 and Leu606, all of which make close hydrophobic contacts with the second Phe (F2) of the core. Phe603 and Ile612 are slightly more distant from Phe F2, but probably also contribute to the hydrophobic interface. The first Phe of the repeat core, F1, appears to shield the hydrophobic portions of the side-chains of Glu611 and Pro613 from solvent and thus probably also contributes to the interaction interface.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 326, 849-858) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21822283 M.Teplova, L.Wohlbold, N.W.Khin, E.Izaurralde, and D.J.Patel (2011).
Structure-function studies of nucleocytoplasmic transport of retroviral genomic RNA by mRNA export factor TAP.
  Nat Struct Mol Biol, 18, 990-998.
PDB codes: 3rw6 3rw7
20421988 L.J.Colwell, M.P.Brenner, and K.Ribbeck (2010).
Charge as a selection criterion for translocation through the nuclear pore complex.
  PLoS Comput Biol, 6, e1000747.  
20005110 V.O.Wickramasinghe, P.I.McMurtrie, A.D.Mills, Y.Takei, S.Penrhyn-Lowe, Y.Amagase, S.Main, J.Marr, M.Stewart, and R.A.Laskey (2010).
mRNA export from mammalian cell nuclei is dependent on GANP.
  Curr Biol, 20, 25-31.  
19219046 H.von Moeller, C.Basquin, and E.Conti (2009).
The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner.
  Nat Struct Mol Biol, 16, 247-254.
PDB codes: 3fhc 3fht
19801417 L.J.Terry, and S.R.Wente (2009).
Flexible gates: dynamic topologies and functions for FG nucleoporins in nucleocytoplasmic transport.
  Eukaryot Cell, 8, 1814-1827.  
19401465 M.Hobeika, C.Brockmann, F.Gruessing, D.Neuhaus, G.Divita, M.Stewart, and C.Dargemont (2009).
Structural requirements for the ubiquitin-associated domain of the mRNA export factor Mex67 to bind its specific targets, the transcription elongation THO complex component Hpr1 and nucleoporin FXFG repeats.
  J Biol Chem, 284, 17575-17583.
PDB code: 2khh
19748337 S.G.Brohawn, J.R.Partridge, J.R.Whittle, and T.U.Schwartz (2009).
The nuclear pore complex has entered the atomic age.
  Structure, 17, 1156-1168.  
17978099 L.H.Matzat, S.Berberoglu, and L.Lévesque (2008).
Formation of a Tap/NXF1 Homotypic Complex Is Mediated through the Amino-Terminal Domain of Tap and Enhances Interaction with Nucleoporins.
  Mol Biol Cell, 19, 327-338.  
18228033 R.Y.Lim, U.Aebi, and B.Fahrenkrog (2008).
Towards reconciling structure and function in the nuclear pore complex.
  Histochem Cell Biol, 129, 105-116.  
17506639 A.Cook, F.Bono, M.Jinek, and E.Conti (2007).
Structural biology of nucleocytoplasmic transport.
  Annu Rev Biochem, 76, 647-671.  
17475778 M.Hobeika, C.Brockmann, N.Iglesias, C.Gwizdek, D.Neuhaus, F.Stutz, M.Stewart, G.Divita, and C.Dargemont (2007).
Coordination of Hpr1 and ubiquitin binding by the UBA domain of the mRNA export factor Mex67.
  Mol Biol Cell, 18, 2561-2568.
PDB code: 2jp7
17287812 M.Stewart (2007).
Molecular mechanism of the nuclear protein import cycle.
  Nat Rev Mol Cell Biol, 8, 195-208.  
16421734 A.S.Madrid, and K.Weis (2006).
Nuclear transport is becoming crystal clear.
  Chromosoma, 115, 98.  
17056718 C.Gwizdek, N.Iglesias, M.S.Rodriguez, B.Ossareh-Nazari, M.Hobeika, G.Divita, F.Stutz, and C.Dargemont (2006).
Ubiquitin-associated domain of Mex67 synchronizes recruitment of the mRNA export machinery with transcription.
  Proc Natl Acad Sci U S A, 103, 16376-16381.  
16314397 L.Lévesque, Y.C.Bor, L.H.Matzat, L.Jin, S.Berberoglu, D.Rekosh, M.L.Hammarskjöld, and B.M.Paschal (2006).
Mutations in tap uncouple RNA export activity from translocation through the nuclear pore complex.
  Mol Biol Cell, 17, 931-943.  
16402261 R.Y.Lim, U.Aebi, and D.Stoffler (2006).
From the trap to the basket: getting to the bottom of the nuclear pore complex.
  Chromosoma, 115, 15-26.  
16000379 F.Kendirgi, D.J.Rexer, A.R.Alcázar-Román, H.M.Onishko, and S.R.Wente (2005).
Interaction between the shuttling mRNA export factor Gle1 and the nucleoporin hCG1: a conserved mechanism in the export of Hsp70 mRNA.
  Mol Biol Cell, 16, 4304-4315.  
15813752 R.Peters (2005).
Translocation through the nuclear pore complex: selectivity and speed by reduction-of-dimensionality.
  Traffic, 6, 421-427.  
14729961 D.Forler, G.Rabut, F.D.Ciccarelli, A.Herold, T.Köcher, R.Niggeweg, P.Bork, J.Ellenberg, and E.Izaurralde (2004).
RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export.
  Mol Cell Biol, 24, 1155-1167.  
15029246 X.Yuan, P.Simpson, C.McKeown, H.Kondo, K.Uchiyama, R.Wallis, I.Dreveny, C.Keetch, X.Zhang, C.Robinson, P.Freemont, and S.Matthews (2004).
Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97.
  EMBO J, 23, 1463-1473.
PDB codes: 1v92 1vaz
14517553 J.A.Floyd, D.A.Gold, D.Concepcion, T.H.Poon, X.Wang, E.Keithley, D.Chen, E.J.Ward, S.B.Chinn, R.A.Friedman, H.T.Yu, K.Moriwaki, T.Shiroishi, and B.A.Hamilton (2003).
A natural allele of Nxf1 suppresses retrovirus insertional mutations.
  Nat Genet, 35, 221-228.  
12835756 S.Fribourg, and E.Conti (2003).
Structural similarity in the absence of sequence homology of the messenger RNA export factors Mtr2 and p15.
  EMBO Rep, 4, 699-703.
PDB code: 1of5
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.