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PDBsum entry 2u1a

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protein links
Nuclear protein PDB id
2u1a
Jmol
Contents
Protein chain
88 a.a. *
* Residue conservation analysis
PDB id:
2u1a
Name: Nuclear protein
Title: RNA binding domain 2 of human u1a protein, nmr, 20 structures
Structure: U1 small nuclear ribonucleoprotein a. Chain: a. Fragment: RNA binding domain 2, rbd2. Synonym: u1 snrnp a protein. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pha. Expressed in: escherichia coli str. K-12 substr. Mg1655. Expression_system_taxid: 511145.
NMR struc: 20 models
Authors: J.Lu,K.B.Hall
Key ref:
J.Lu and K.B.Hall (1997). Tertiary structure of RBD2 and backbone dynamics of RBD1 and RBD2 of the human U1A protein determined by NMR spectroscopy. Biochemistry, 36, 10393-10405. PubMed id: 9265619 DOI: 10.1021/bi9709811
Date:
26-Mar-97     Release date:   26-Sep-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P09012  (SNRPA_HUMAN) -  U1 small nuclear ribonucleoprotein A
Seq:
Struc:
282 a.a.
88 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nuclear mRNA splicing, via spliceosome   1 term 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1021/bi9709811 Biochemistry 36:10393-10405 (1997)
PubMed id: 9265619  
 
 
Tertiary structure of RBD2 and backbone dynamics of RBD1 and RBD2 of the human U1A protein determined by NMR spectroscopy.
J.Lu, K.B.Hall.
 
  ABSTRACT  
 
The human U1A protein has two putative RNA binding domains, one at the N-terminal region of the protein (RBD1) and the other at the C-terminal end (RBD2). RBD1 binds tightly and specifically to one of the stem loops of the U1 snRNA, as well as to its own 3'-UTR. In contrast, RBD2 does not appear to associate with any RNA. The two domains share 25% amino acid identity, and both have the same betaalphabeta-betaalphabeta secondary structure fold. In this work, 13C/15N/1H multidimensional NMR methods were used to obtain side-chain assignments for RBD2, and then the tertiary structure was calculated using a distance geometry/simulated annealing algorithm that employs pairwise Gaussian metrization. RBD2 is shown to fold into an alpha/beta sandwich with a four-stranded antiparallel beta-sheet, which is the typical global topology of these domains. Specific structural features of RBD2 include a beta-bulge in beta2, N-capping boxes for both alpha-helices, and an extremely shallow twist of its beta-sheet. The 15N backbone dynamics of these two structurally homologous RBDs are significantly different, compared using order parameters and T2 exchange terms in the Lipari and Szabo model-free formalism. Conformational exchange observed in RBD1, which is absent in RBD2, may correlate to the mechanism of RNA binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20080103 C.M.Maynard, and K.B.Hall (2010).
Interactions between PTB RRMs induce slow motions and increase RNA binding affinity.
  J Mol Biol, 397, 260-277.  
19000813 J.Sperling, M.Azubel, and R.Sperling (2008).
Structure and function of the Pre-mRNA splicing machine.
  Structure, 16, 1605-1615.  
15951381 S.A.Showalter, and K.B.Hall (2005).
Correlated motions in the U1 snRNA stem/loop 2:U1A RBD1 complex.
  Biophys J, 89, 2046-2058.  
12809490 G.C.Pérez-Alvarado, M.Martínez-Yamout, M.M.Allen, R.Grosschedl, H.J.Dyson, and P.E.Wright (2003).
Structure of the nuclear factor ALY: insights into post-transcriptional regulatory and mRNA nuclear export processes.
  Biochemistry, 42, 7348-7357.
PDB code: 1no8
12730685 S.Fribourg, D.Gatfield, E.Izaurralde, and E.Conti (2003).
A novel mode of RBD-protein recognition in the Y14-Mago complex.
  Nat Struct Biol, 10, 433-439.
PDB code: 1hl6
12203842 C.S.Lutz, M.T.McClain, J.B.Harley, and J.A.James (2002).
Anti-U1A monoclonal antibodies recognize unique epitope targets of U1A which are involved in the binding of U1 RNA.
  J Mol Recognit, 15, 163-170.  
12434430 F.Pitici, D.L.Beveridge, and A.M.Baranger (2002).
Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: do molecular substates code for specificity?
  Biopolymers, 65, 424-435.  
11179892 J.M.Pérez-Cañadillas, and G.Varani (2001).
Recent advances in RNA-protein recognition.
  Curr Opin Struct Biol, 11, 53-58.  
10852733 C.Clerte, and K.B.Hall (2000).
Spatial orientation and dynamics of the U1A proteins in the U1A-UTR complex.
  Biochemistry, 39, 7320-7329.  
11032824 S.Nanduri, F.Rahman, B.R.Williams, and J.Qin (2000).
A dynamically tuned double-stranded RNA binding mechanism for the activation of antiviral kinase PKR.
  EMBO J, 19, 5567-5574.  
10024175 C.M.Reyes, and P.A.Kollman (1999).
Molecular dynamics studies of U1A-RNA complexes.
  RNA, 5, 235-244.  
  10548057 J.M.Jean, C.Clerte, and K.B.Hall (1999).
Global and local dynamics of the human U1A protein determined by tryptophan fluorescence.
  Protein Sci, 8, 2110-2120.  
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 code is shown on the right.