5DEA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


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

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

  • 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 ...

    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.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016; pateld@mskcc.org Alexander.Serganov@nyumc.org.



Macromolecules

  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fragile X mental retardation protein 1BD18Homo sapiensMutation(s): 0 
Gene Names: FMR1
Find proteins for Q06787 (Homo sapiens)
Explore Q06787 
Go to UniProtKB:  Q06787
NIH Common Fund Data Resources
PHAROS  Q06787
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
sc1A, C35synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CS
Query on CS

Download CCD File 
A, C
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.57α = 90
b = 129.87β = 90
c = 36.79γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103403
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesR21MH103655
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesTR01 GM104962
Whitehead Institute for Biomedical ResearchUnited States--
Edward Mallinckrodt, Jr. FoundationUnited States--
New York UniversityUnited 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