Summary information

PDB id
2la5
Class
RNA binding protein-RNA
Method
NMR
Summary
RNA duplex-quadruplex junction complex with fmrp rgg peptide
Reference
Phan AT, Kuryavyi V, Darnell JC, Serganov A, Majumdar A, Ilin S, Raslin T, Polonskaia A, Chen C, Clain D, Darnell RB, Patel DJ (2011): "Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction." Nat.Struct.Mol.Biol., 18, 796-804. doi: 10.1038/nsmb.2064.
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.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.176 type=other  nts=4 GGGG A.G6,A.G9,A.G26,A.G18
 2 glyco-bond=---- sugar=3--- groove=---- planarity=0.195 type=other  nts=4 GGGG A.G11,A.G15,A.G20,A.G24
 3 glyco-bond=---- sugar=---3 groove=---- planarity=0.106 type=planar nts=4 GGGG A.G12,A.G16,A.G21,A.G25

List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 3 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.G6,A.G9,A.G26,A.G18
 2  glyco-bond=---- sugar=--3- groove=---- Major-->WC nts=4 GGGG A.G16,A.G12,A.G25,A.G21
 3  glyco-bond=---- sugar=-3-- groove=---- Major-->WC nts=4 GGGG A.G15,A.G11,A.G24,A.G20
  step#1  pp(><,inward)   area=11.21 rise=3.33 twist=-40.0
  step#2  mp(<<,backward) area=12.11 rise=3.44 twist=30.4
  strand#1 RNA glyco-bond=--- sugar=--- nts=3 GGG A.G6,A.G16,A.G15
  strand#2 RNA glyco-bond=--- sugar=--3 nts=3 GGG A.G9,A.G12,A.G11
  strand#3 RNA glyco-bond=--- sugar=-3- nts=3 GGG A.G26,A.G25,A.G24
  strand#4 RNA glyco-bond=--- sugar=--- nts=3 GGG A.G18,A.G21,A.G20

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.G6,A.G9,A.G26,A.G18
 2  glyco-bond=---- sugar=--3- groove=---- Major-->WC nts=4 GGGG A.G16,A.G12,A.G25,A.G21
  step#1  pp(><,inward)   area=11.21 rise=3.33 twist=-40.0

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 2  glyco-bond=---- sugar=--3- groove=---- Major-->WC nts=4 GGGG A.G16,A.G12,A.G25,A.G21
 3  glyco-bond=---- sugar=-3-- groove=---- Major-->WC nts=4 GGGG A.G15,A.G11,A.G24,A.G20
  step#2  mp(<<,backward) area=12.11 rise=3.44 twist=30.4

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List of 1 G4-stem

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=3--- groove=---- WC-->Major nts=4 GGGG A.G11,A.G15,A.G20,A.G24
 2  glyco-bond=---- sugar=---3 groove=---- WC-->Major nts=4 GGGG A.G12,A.G16,A.G21,A.G25
  step#1  pm(>>,forward)  area=12.11 rise=3.44 twist=30.4
  strand#1  U RNA glyco-bond=-- sugar=3- nts=2 GG A.G11,A.G12
  strand#2  U RNA glyco-bond=-- sugar=-- nts=2 GG A.G15,A.G16
  strand#3  U RNA glyco-bond=-- sugar=-- nts=2 GG A.G20,A.G21
  strand#4  U RNA glyco-bond=-- sugar=-3 nts=2 GG A.G24,A.G25
  loop#1 type=propeller strands=[#1,#2] nts=2 AA A.A13,A.A14
  loop#2 type=propeller strands=[#2,#3] nts=3 AGU A.A17,A.G18,A.U19
  loop#3 type=propeller strands=[#3,#4] nts=2 CU A.C22,A.U23

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List of 1 non-stem G4-loop (including the two closing Gs)

 1 type=lateral   helix=#1 nts=4 GGUG A.G6,A.G7,A.U8,A.G9