PDBsum entry 1hd1

Go to PDB code: 
protein links
RNA binding protein PDB id
Protein chain
75 a.a. *
* Residue conservation analysis
PDB id:
Name: RNA binding protein
Title: Heterogeneous nuclear ribonucleoprotein d0 (hnrnp d0 rbd1), nmr
Structure: Protein (heterogeneous nuclear ribonucleoprotein d0). Chain: a. Fragment: RNA-binding domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cell: hela. Cellular_location: nucleus. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_cell: bl21(de3). Other_details: pcr
NMR struc: 20 models
Authors: T.Nagata,Y.Kurihara,G.Matsuda,J.Saeki,T.Kohno,Y.Yanagida, F.Ishikawa,S.Uesugi,M.Katahira
Key ref:
T.Nagata et al. (1999). Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0. J Mol Biol, 287, 221-237. PubMed id: 10080887 DOI: 10.1006/jmbi.1999.2616
18-May-99     Release date:   18-May-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q14103  (HNRPD_HUMAN) -  Heterogeneous nuclear ribonucleoprotein D0
355 a.a.
75 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     2 terms  


DOI no: 10.1006/jmbi.1999.2616 J Mol Biol 287:221-237 (1999)
PubMed id: 10080887  
Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0.
T.Nagata, Y.Kurihara, G.Matsuda, J.Saeki, T.Kohno, Y.Yanagida, F.Ishikawa, S.Uesugi, M.Katahira.
Heterogeneous nuclear ribonucleoprotein (hnRNP) D0 has two ribonucleoprotein (RNP)-type RNA-binding domains (RBDs), each of which can bind solely to the UUAG sequence specifically. The structure of the N-terminal RBD (RBD1) determined by NMR is presented here. It folds into a compact alphabeta structure comprising a four-stranded antiparallel beta-sheet packed against two alpha-helices, which is characteristic of the RNP-type RBDs. Special structural features of RBD1 include N-capping boxes for both alpha-helices, a beta-bulge in the second beta-strand, and an additional short antiparallel beta-sheet coupled with a beta-turn-like structure in a loop. Two hydrogen bonds which restrict the positions of loops were identified. Backbone resonance assignments for RBD1 complexed with r(UUAGGG) revealed that the overall folding is maintained in the complex. The candidate residues involved in the interactions with RNA were identified by chemical shift perturbation analysis. They are located in the central and peripheral regions of the RNA-binding surface composed of the four-stranded beta-sheet, loops, and the C-terminal region. It is suggested that non-specific interactions with RNA are performed by the residues in the central region of the RNA-binding surface, while specific interactions are performed by those in the peripheral regions. It was also found that RBD1 has the ability to inhibit the formation of the quadruplex structure.
  Selected figure(s)  
Figure 2.
Figure 2. The four-stranded antiparallel β-sheet of p112. Interstrand NOEs are indicated by double-headed arrows. Slowly exchanging amide protons are indicated by bold Hs. Hydrogen bonds consistent with the NOEs and exchange data are indicated by broken lines. Circles for C^α indicate that the side-chains of these residues are presumed to be exposed to the solvent.
Figure 3.
Figure 3. The structure of the 29–103 region of p112. (a) Superposition of the main-chains of 20 refined structures for the residues 29–103. N and C indicate K29 and A103, respectively, and loop 3 is labeled. (b) Schematic drawing of the restrained energy minimized mean structure derived from the 20 refined structures for 29–103, as viewed from the same direction as in (a). (c) Hydrophobic core. Overlaying of the 20 structures of the side-chains for residues involved in the hydrophobic core is shown on the main-chain of the restrained energy minimized mean structure. The α-helices and β-strands are colored in red and blue, respectively. (d) Hydrophobic patch exposed to the solvent. The same overlaying as in (c) is shown for F31, F71 and F73, being rotated by ca. 90 ° from (c).
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 287, 221-237) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
19422301 S.Pan, L.Cheng, J.T.White, W.Lu, A.G.Utleg, X.Yan, N.D.Urban, C.W.Drescher, L.Hood, and B.Lin (2009).
Quantitative proteomics analysis integrated with microarray data reveals that extracellular matrix proteins, catenins, and p53 binding protein 1 are important for chemotherapy response in ovarian cancers.
  OMICS, 13, 345-354.  
18641416 T.Nagata, S.Suzuki, R.Endo, M.Shirouzu, T.Terada, M.Inoue, T.Kigawa, N.Kobayashi, P.Güntert, A.Tanaka, Y.Hayashizaki, Y.Muto, and S.Yokoyama (2008).
The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.
  Nucleic Acids Res, 36, 4754-4767.
PDB code: 2rok
18953025 T.Nagata, Y.Takada, A.Ono, K.Nagata, Y.Konishi, T.Nukina, M.Ono, A.Matsugami, A.Furukawa, N.Fujimoto, H.Fukuda, H.Nakagama, and M.Katahira (2008).
Elucidation of the mode of interaction in the UP1-telomerase RNA-telomeric DNA ternary complex which serves to recruit telomerase to telomeric DNA and to enhance the telomerase activity.
  Nucleic Acids Res, 36, 6816-6824.  
15724445 A.Bandiera, N.Medic, A.A.Akindahunsi, and G.Manzini (2005).
In-vitro dual binding activity of a evolutionarily related subgroup of hnRNP proteins.
  Mol Cell Biochem, 268, 121-127.  
15734733 Y.Enokizono, Y.Konishi, K.Nagata, K.Ouhashi, S.Uesugi, F.Ishikawa, and M.Katahira (2005).
Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D.
  J Biol Chem, 280, 18862-18870.
PDB codes: 1wtb 1x0f
15004549 C.Alfano, D.Sanfelice, J.Babon, G.Kelly, A.Jacks, S.Curry, and M.R.Conte (2004).
Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein.
  Nat Struct Mol Biol, 11, 323-329.
PDB codes: 1s79 1s7a
12773396 J.M.Pérez Cañadillas, and G.Varani (2003).
Recognition of GU-rich polyadenylation regulatory elements by human CstF-64 protein.
  EMBO J, 22, 2821-2830.
PDB code: 1p1t
12907678 Y.Miyanoiri, H.Kobayashi, T.Imai, M.Watanabe, T.Nagata, S.Uesugi, H.Okano, and M.Katahira (2003).
Origin of higher affinity to RNA of the N-terminal RNA-binding domain than that of the C-terminal one of a mouse neural protein, musashi1, as revealed by comparison of their structures, modes of interaction, surface electrostatic potentials, and backbone dynamics.
  J Biol Chem, 278, 41309-41315.
PDB code: 1uaw
12108548 K.C.Moraes, W.H.Lee, and J.Kobarg (2002).
Analysis of the structural determinants for RNA binding of the human protein AUF1/hnRNP D.
  Biol Chem, 383, 831-837.  
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.