Macromolecule Content

• Total Structure Weight: 8.57 kDa 
• Atom Count: 601 
• Residue Count: 75 
• Unique protein chains: 1

1HD0

HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN D0 (HNRNP D0 RBD1), NMR

• DOI: 10.2210/pdb1HD0/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1999-05-18 Released: 2000-05-18 
• Deposition Author(s): Nagata, T., Kurihara, Y., Matsuda, G., Saeki, J., Kohno, T., Yanagida, Y., Ishikawa, F., Uesugi, S., Katahira, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 1 
• Selection Criteria: LOWER ENERGIES 

Literature

Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0.

Nagata, T., Kurihara, Y., Matsuda, G., Saeki, J., Kohno, T., Yanagida, Y., Ishikawa, F., Uesugi, S., Katahira, M.

(1999) J Mol Biol 287: 221-237

• PubMed: 10080887 
• DOI: 10.1006/jmbi.1999.2616
• Primary Citation of Related Structures:  
  1HD1, 1HD0


• PubMed Abstract: 
  

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.

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Organizational Affiliation: 

Department of Chemistry and Biotechnology, Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN D0)	A	75	Homo sapiens	Mutation(s): 0  Gene Names: HNRNPD, AUF1, HNRPD
Find proteins for Q14103 (Homo sapiens) Explore Q14103  Go to UniProtKB:  Q14103
NIH Common Fund Data Resources
PHAROS:  Q14103 GTEx:  ENSG00000138668

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 1 
• Selection Criteria: LOWER ENERGIES 
• OLDERADO: 1HD0 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-05-18 
• Released Date: 2000-05-18 
Deposition Author(s): Nagata, T., Kurihara, Y., Matsuda, G., Saeki, J., Kohno, T., Yanagida, Y., Ishikawa, F., Uesugi, S., Katahira, M.

Revision History 

• Version 1.0: 2000-05-18
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance