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PDBsum entry 1g2e

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protein dna_rna links
Transcription/RNA PDB id
1g2e
Jmol
Contents
Protein chain
167 a.a. *
DNA/RNA
Waters ×154
* Residue conservation analysis
PDB id:
1g2e
Name: Transcription/RNA
Title: Crystal structure of hud and au-rich element of the tumor necrosis factor alpha RNA
Structure: 5'-r(p Up Ap Up Up Up Ap Up Up Up A)-3'. Chain: b. Fragment: fragment of au-rich element of the tumor necrosis factor alpha RNA. Engineered: yes. Paraneoplastic encephalomyelitis antigen hud. Chain: a. Fragment: n-terminal two rrm-domains. Engineered: yes
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Organ: brain. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.174     R-free:   0.238
Authors: X.Wang,T.M.T.Hall
Key ref:
X.Wang and T.M.Tanaka Hall (2001). Structural basis for recognition of AU-rich element RNA by the HuD protein. Nat Struct Biol, 8, 141-145. PubMed id: 11175903 DOI: 10.1038/84131
Date:
18-Oct-00     Release date:   05-Feb-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26378  (ELAV4_HUMAN) -  ELAV-like protein 4
Seq:
Struc:
380 a.a.
167 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1038/84131 Nat Struct Biol 8:141-145 (2001)
PubMed id: 11175903  
 
 
Structural basis for recognition of AU-rich element RNA by the HuD protein.
X.Wang, T.M.Tanaka Hall.
 
  ABSTRACT  
 
Hu proteins bind to adenosine-uridine (AU)-rich elements (AREs) in the 3' untranslated regions of many short-lived mRNAs, thereby stabilizing them. Here we report the crystal structures of the first two RNA recognition motif (RRM) domains of the HuD protein in complex with an 11-nucleotide fragment of a class I ARE (the c-fos ARE; to 1.8 A), and with an 11-nucleotide fragment of a class II ARE (the tumor necrosis factor alpha ARE; to 2.3 A). These structures reveal a consensus RNA recognition sequence that suggests a preference for pyrimidine-rich sequences and a requirement for a central uracil residue in the clustered AUUUA repeats found in class II AREs. Comparison to structures of other RRM domain-nucleic acid complexes reveals two base recognition pockets in all the structures that interact with bases using residues in conserved ribonucleoprotein motifs and at the C-terminal ends of RRM domains. Different conformations of nucleic acid can be bound by RRM domains by using different combinations of base recognition pockets and multiple RRM domains.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Protein -RNA contacts. a, Stereo diagram of the cfos-11 structure and HuD1,2 side chain contacts. b, Stereo diagram of the TNF 11 structure and HuD1,2 side chain contacts. The structures of the cfos-11 and TNF 11 RNAs are shown as ball-and-stick models colored by atom type. The bases and 5' and 3' ends of the RNA and side chains contacting the RNA are labeled. 2F[o] - F[c] maps for the cfos-11 and TNF 11 RNAs contoured at 1 are shown superimposed on their respective ball-and-stick models. Two water molecules are shown as green spheres. Hydrogen bonds within the RNA structures and with the water molecules are shown as black dotted lines and hydrogen bonds between the protein and RNAs are shown as red dashed lines. Amino acid residues are colored as in Fig. 1b. c, Summary of contacts between HuD1,2 protein and cfos-11 RNA. d, Summary of contacts between HuD1,2 protein and TNF 11 RNA. Red lines indicate side chain contacts, green lines indicate main chain contacts, and dashed orange lines indicate stacking interactions. Distances in Ć are noted. Atoms on the RNA that are recognized in water-mediated contacts are highlighted with yellow. In the complex with TNF 11, the side chains of Tyr 128, Arg 166 and Lys 201 and the main chain of A203 seem to have moved away from the RNA to accommodate the A3 base. This could indicate plasticity in this site or reflect the ability to accommodate a less than ideal sequence at the concentration used for crystallization (1 mM).
Figure 4.
Figure 4. Nucleic acid recognition by RRM domains. a, Stereo diagram showing the superposition of RRM domains from HuD, Sxl, PABP, UP1, U1A, and U2B". The bases in all the structures at positions equivalent to U3/U9 (Sxl, G4/U10; PABP, A3/A6; UP1, A203/A209; U1A, C10; and U2B", C10) and U4/U10 (Sxl, U5/U11; PABP, A4/A8; UP1, G204/G210; U1A, A11; and U2B", A11) in the HuD1,2 -cfos-11 structure are shown in yellow and blue, respectively. Amino acid side chains at positions equivalent to Asn 40/Asn 126 (Sxl, Asn 126/Asn 212; PABP, Ser 12/Asn 100; and UP1, Lys 15/Lys 106), Ile 42/Tyr 128 (Sxl, Ile 124/Tyr 214; PABP, Tyr 14/Phe 102; UP1, Phe 17/Phe 108; U1A, Tyr 13; and U2B", Tyr 13), and Phe 84/Phe 170 (Sxl, Phe 170/Phe 256; PABP, Tyr 56/Phe 142; UP1, Phe 59/Phe 150; U1A, Phe 56; and U2B", Phe 56) in HuD1,2 are shown and backbone atoms at positions equivalent to Arg 116/Ala 203 of HuD1,2 (Sxl, Arg 202/Ala 289; PABP, Gln 88/Phe 173; UP1, Val 90/Leu 181; U1A, Lys 88; and U2B", Lys 88) are shown. Amino acid residues are colored as in Fig 1b. The side chains of Thr 11 in U1A and U2B", which occupy positions structurally equivalent to Asn 40/126 of HuD1,2, do not contact the RNA. Instead the side chains of Ser 91 near the C-terminus of U1A and U2B", which have no structural equivalent in the other structures, contact the RNA. b, Base recognition in the U3/U9 binding pocket. Stereo view showing the superimposed ball-and-stick models of U3 in the HuD1,2 -cfos-11 structure (green), G4 in the Sxl -tra structure (yellow), A209 in the UP1 -telomeric DNA structure (blue), and C10 in the U1A -U1 RNA structure (orange) and the residues contacting the bases. c, Base recognition in the U4/U10 binding pocket. Stereo view showing the superimposed ball-and-stick models of U10 in the HuD1,2 -cfos-11 structure (green), U5 in the Sxl -tra structure (yellow), A8 in the PABP -A[11] structure (red), and G204 in the UP1 -telomeric DNA structure (blue) and the residues contacting the bases. Hydrogen bonds are indicated by dotted lines.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 141-145) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21419778 D.Anunciado, A.Dhar, M.Gruebele, and A.M.Baranger (2011).
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PDB codes: 3q2s 3q2t
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  Biochimie, 93, 817-822.  
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Interactions between PTB RRMs induce slow motions and increase RNA binding affinity.
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Novel recognition motifs and biological functions of the RNA-binding protein HuD revealed by genome-wide identification of its targets.
  Nucleic Acids Res, 38, 117-130.  
20479262 Q.Yang, G.M.Gilmartin, and S.Doublié (2010).
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PDB codes: 3mdg 3mdi
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  Mol Cell, 36, 1007-1017.  
  19255485 D.Iyaguchi, M.Yao, I.Tanaka, and E.Toyota (2009).
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Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3.
  Nucleic Acids Res, 37, 5151-5166.
PDB codes: 2rq4 2rqc
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PDB code: 3d2w
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PDB code: 2qfj
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PDB codes: 2nrq 2nwu 2ogk 2pzz
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PDB code: 2cjk
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Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface.
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Shared RNA-binding sites for interacting members of the Drosophila ELAV family of neuronal proteins.
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ELAV multimerizes on conserved AU4-6 motifs important for ewg splicing regulation.
  Mol Cell Biol, 25, 7580-7591.  
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RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle.
  EMBO Rep, 6, 33-38.  
15853794 Y.Chen, and G.Varani (2005).
Protein families and RNA recognition.
  FEBS J, 272, 2088-2097.  
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The androgen receptor mRNA.
  Bioessays, 26, 672-682.  
14981510 B.P.Hudson, M.A.Martinez-Yamout, H.J.Dyson, and P.E.Wright (2004).
Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d.
  Nat Struct Mol Biol, 11, 257-264.
PDB code: 1rgo
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The splicing factor U2AF small subunit is functionally conserved between fission yeast and humans.
  Mol Cell Biol, 24, 4229-4240.  
15231733 C.L.Kielkopf, S.Lücke, and M.R.Green (2004).
U2AF homology motifs: protein recognition in the RRM world.
  Genes Dev, 18, 1513-1526.  
15226427 K.L.Carroll, D.A.Pradhan, J.A.Granek, N.D.Clarke, and J.L.Corden (2004).
Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts.
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15457527 N.C.Meisner, J.Hackermüller, V.Uhl, A.Aszódi, M.Jaritz, and M.Auer (2004).
mRNA openers and closers: modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure.
  Chembiochem, 5, 1432-1447.  
15192703 N.Leulliot, S.Quevillon-Cheruel, M.Graille, H.van Tilbeurgh, T.C.Leeper, K.S.Godin, T.E.Edwards, S.T.Sigurdsson, N.Rozenkrants, R.J.Nagel, M.Ares, and G.Varani (2004).
A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III.
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PDB codes: 1t4n 1t4o
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Visualizing the RNA molecule in the bacterially expressed vesicular stomatitis virus nucleoprotein-RNA complex.
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Neuronal HuD gene encoding a mRNA stability regulator is transcriptionally repressed by thyroid hormone.
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Structure of the nuclear factor ALY: insights into post-transcriptional regulatory and mRNA nuclear export processes.
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PDB code: 1no8
12554879 H.Banerjee, A.Rahn, W.Davis, and R.Singh (2003).
Sex lethal and U2 small nuclear ribonucleoprotein auxiliary factor (U2AF65) recognize polypyrimidine tracts using multiple modes of binding.
  RNA, 9, 88-99.  
12773396 J.M.Pérez Cañadillas, and G.Varani (2003).
Recognition of GU-rich polyadenylation regulatory elements by human CstF-64 protein.
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PDB code: 1p1t
12595544 M.I.Zarudnaya, I.M.Kolomiets, A.L.Potyahaylo, and D.M.Hovorun (2003).
Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures.
  Nucleic Acids Res, 31, 1375-1386.  
14506271 O.A.Kent, A.Reayi, L.Foong, K.A.Chilibeck, and A.M.MacMillan (2003).
Structuring of the 3' splice site by U2AF65.
  J Biol Chem, 278, 50572-50577.  
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Characterization of the interaction between neuronal RNA-binding protein HuD and AU-rich RNA.
  J Biol Chem, 278, 39801-39808.  
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The RNA-binding protein HuR regulates the expression of cyclooxygenase-2.
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Transterm: a database of mRNAs and translational control elements.
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12466552 J.B.Tuite, J.C.Shiels, and A.M.Baranger (2002).
Substitution of an essential adenine in the U1A-RNA complex with a non-polar isostere.
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Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1.
  Nucleic Acids Res, 30, 1531-1538.
PDB code: 1l3k
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Expression of the human RNA-binding protein HuR in Trypanosoma brucei increases the abundance of mRNAs containing AU-rich regulatory elements.
  Nucleic Acids Res, 30, 4414-4424.  
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Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein.
  EMBO J, 21, 3546-3556.
PDB codes: 1kq1 1kq2
12082087 P.S.Katsamba, M.Bayramyan, I.S.Haworth, D.G.Myszka, and I.A.Laird-Offringa (2002).
Complex role of the beta 2-beta 3 loop in the interaction of U1A with U1 hairpin II RNA.
  J Biol Chem, 277, 33267-33274.  
12409457 S.Bonnet-Corven, Y.Audic, F.Omilli, and H.B.Osborne (2002).
An analysis of the sequence requirements of EDEN-BP for specific RNA binding.
  Nucleic Acids Res, 30, 4667-4674.  
12121976 S.Horke, K.Reumann, A.Rang, and T.Heise (2002).
Molecular characterization of the human La protein.hepatitis B virus RNA.B interaction in vitro.
  J Biol Chem, 277, 34949-34958.  
11788707 X.Yuan, N.Davydova, M.R.Conte, S.Curry, and S.Matthews (2002).
Chemical shift mapping of RNA interactions with the polypyrimidine tract binding protein.
  Nucleic Acids Res, 30, 456-462.  
11551507 C.L.Kielkopf, N.A.Rodionova, M.R.Green, and S.K.Burley (2001).
A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer.
  Cell, 106, 595-605.
PDB code: 1jmt
11545740 C.Mazza, M.Ohno, A.Segref, I.W.Mattaj, and S.Cusack (2001).
Crystal structure of the human nuclear cap binding complex.
  Mol Cell, 8, 383-396.
PDB code: 1h6k
11581160 M.J.Lisbin, J.Qiu, and K.White (2001).
The neuron-specific RNA-binding protein ELAV regulates neuroglian alternative splicing in neurons and binds directly to its pre-mRNA.
  Genes Dev, 15, 2546-2561.  
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.