Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.56 kDa 
• Atom Count: 904 
• Modelled Residue Count: 53 
• Deposited Residue Count: 53 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2LA5

RNA Duplex-Quadruplex Junction Complex with FMRP RGG peptide

• PDB DOI: 10.2210/pdb2LA5/pdb
• BMRB: 17504
• NDB: 2LA5

• Classification: RNA Binding Protein/RNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2011-03-03 Released: 2011-06-08 
• Deposition Author(s): Phan, A., Kuryavyi, V., Darnell, J., Serganov, A., Majumdar, A., Ilin, S., Darnell, R., Patel, D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction.

Phan, A.T., Kuryavyi, V., Darnell, J.C., Serganov, A., Majumdar, A., Ilin, S., Raslin, T., Polonskaia, A., Chen, C., Clain, D., Darnell, R.B., Patel, D.J.

(2011) Nat Struct Mol Biol 18: 796-804

• PubMed: 21642970 
• DOI: 10.1038/nsmb.2064
• Primary Citation of Related Structures:  
  2LA5


• PubMed Abstract: 
  

We have determined the solution structure of the complex between an arginine-glycine-rich RGG peptide from the human fragile X mental retardation protein (FMRP) and an in vitro-selected guanine-rich (G-rich) sc1 RNA. The bound RNA forms a newly discovered G-quadruplex separated from the flanking duplex stem by a mixed junctional tetrad. The RGG peptide is positioned along the major groove of the RNA duplex, with the G-quadruplex forcing a sharp turn of R(10)GGGGR(15) at the duplex-quadruplex junction. Arg10 and Arg15 form cross-strand specificity-determining intermolecular hydrogen bonds with the major-groove edges of guanines of adjacent Watson-Crick G•C pairs. Filter-binding assays on RNA and peptide mutations identify and validate contributions of peptide-RNA intermolecular contacts and shape complementarity to molecular recognition. These findings on FMRP RGG domain recognition by a combination of G-quadruplex and surrounding RNA sequences have implications for the recognition of other genomic G-rich RNAs.

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Organizational Affiliation: 

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. [e-mail]

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fragile X mental retardation 1 protein	B	17	Homo sapiens	Mutation(s): 0  Gene Names: FMR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q06787 (Homo sapiens) Explore Q06787  Go to UniProtKB:  Q06787
PHAROS:  Q06787 GTEx:  ENSG00000102081

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (36-MER)	A	36	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2LA5 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-03 
• Released Date: 2011-06-08 
Deposition Author(s): Phan, A., Kuryavyi, V., Darnell, J., Serganov, A., Majumdar, A., Ilin, S., Darnell, R., Patel, D.

Revision History  

• Version 1.0: 2011-06-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-20
  Changes: Database references