Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.77 kDa 
• Atom Count: 1,693 
• Modelled Residue Count: 97 
• Deposited Residue Count: 106 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 5DE5

Crystal structure of the complex between human FMRP RGG motif and G-quadruplex RNA.

• PDB DOI: 10.2210/pdb5DE5/pdb
• NDB: 5DE5

• Classification: RNA binding protein/RNA
• Organism(s): synthetic construct, Homo sapiens
• Mutation(s): No 


• Deposited: 2015-08-25 Released: 2015-09-23 
• Deposition Author(s): Vasilyev, N., Polonskaia, A., Darnell, J.C., Darnell, R.B., Patel, D.J., Serganov, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Mental Health (NIH/NIMH), Whitehead Institute for Biomedical Research, Edward Mallinckrodt, Jr. Foundation, New York University

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.221 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Literature

Crystal structure reveals specific recognition of a G-quadruplex RNA by a beta-turn in the RGG motif of FMRP.

Vasilyev, N., Polonskaia, A., Darnell, J.C., Darnell, R.B., Patel, D.J., Serganov, A.

(2015) Proc Natl Acad Sci U S A 112: E5391-E5400

• PubMed: 26374839 
• DOI: 10.1073/pnas.1515737112
• Primary Citation of Related Structures:  
  5DE5, 5DE8, 5DEA


• PubMed Abstract: 
  

Fragile X Mental Retardation Protein (FMRP) is a regulatory RNA binding protein that plays a central role in the development of several human disorders including Fragile X Syndrome (FXS) and autism. FMRP uses an arginine-glycine-rich (RGG) motif for specific interactions with guanine (G)-quadruplexes, mRNA elements implicated in the disease-associated regulation of specific mRNAs. Here we report the 2.8-Å crystal structure of the complex between the human FMRP RGG peptide bound to the in vitro selected G-rich RNA. In this model system, the RNA adopts an intramolecular K(+)-stabilized G-quadruplex structure composed of three G-quartets and a mixed tetrad connected to an RNA duplex. The RGG peptide specifically binds to the duplex-quadruplex junction, the mixed tetrad, and the duplex region of the RNA through shape complementarity, cation-π interactions, and multiple hydrogen bonds. Many of these interactions critically depend on a type I β-turn, a secondary structure element whose formation was not previously recognized in the RGG motif of FMRP. RNA mutagenesis and footprinting experiments indicate that interactions of the peptide with the duplex-quadruplex junction and the duplex of RNA are equally important for affinity and specificity of the RGG-RNA complex formation. These results suggest that specific binding of cellular RNAs by FMRP may involve hydrogen bonding with RNA duplexes and that RNA duplex recognition can be a characteristic RNA binding feature for RGG motifs in other proteins.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016; [e-mail] [e-mail].

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fragile X mental retardation protein 1	B, D	18	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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
sc1	A, C	35	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	E [auth A], F [auth A], G [auth A], H [auth C], I [auth C], J [auth C], K [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.221 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.06	α = 90
b = 130.01	β = 90
c = 36.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-23 
Deposition Author(s): Vasilyev, N., Polonskaia, A., Darnell, J.C., Darnell, R.B., Patel, D.J., Serganov, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41 GM103403
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	R21MH103655
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	TR01 GM104962
Whitehead Institute for Biomedical Research	United States	--
Edward Mallinckrodt, Jr. Foundation	United States	--
New York University	United States	--

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release
  
• Version 1.1: 2015-09-30
  Changes: Database references
• Version 1.2: 2015-10-14
  Changes: Database references
• Version 1.3: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-11-27
  Changes: Author supporting evidence