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- PDB-2la5: RNA Duplex-Quadruplex Junction Complex with FMRP RGG peptide -

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Basic information

Entry
Database: PDB / ID: 2la5
TitleRNA Duplex-Quadruplex Junction Complex with FMRP RGG peptide
Components
  • Fragile X mental retardation 1 protein
  • RNA (36-MER)
KeywordsRNA Binding Protein/RNA / RNA Binding Protein-RNA complex
Function / homology
Function and homology information


positive regulation of intracellular transport of viral material / regulation of mRNA metabolic process / regulation of translation at presynapse, modulating synaptic transmission / dendritic filopodium / negative regulation of voltage-gated calcium channel activity / host-mediated perturbation of viral RNA genome replication / positive regulation of miRNA-mediated gene silencing / negative regulation of synaptic vesicle exocytosis / poly(G) binding / negative regulation of miRNA-mediated gene silencing ...positive regulation of intracellular transport of viral material / regulation of mRNA metabolic process / regulation of translation at presynapse, modulating synaptic transmission / dendritic filopodium / negative regulation of voltage-gated calcium channel activity / host-mediated perturbation of viral RNA genome replication / positive regulation of miRNA-mediated gene silencing / negative regulation of synaptic vesicle exocytosis / poly(G) binding / negative regulation of miRNA-mediated gene silencing / neuronal ribonucleoprotein granule / negative regulation of long-term synaptic depression / regulation of neuronal action potential / intracellular membraneless organelle / animal organ development / histone H3 reader activity / RNA strand annealing activity / regulation of dendritic spine development / chromocenter / filopodium tip / positive regulation of long-term neuronal synaptic plasticity / regulation of neurotransmitter secretion / regulation of filopodium assembly / N6-methyladenosine-containing RNA reader activity / poly(A) binding / membraneless organelle assembly / siRNA binding / sequence-specific mRNA binding / growth cone filopodium / regulatory ncRNA-mediated gene silencing / positive regulation of filopodium assembly / positive regulation of proteasomal protein catabolic process / miRNA binding / poly(U) RNA binding / positive regulation of dendritic spine development / regulation of alternative mRNA splicing, via spliceosome / glutamate receptor signaling pathway / dynein complex binding / positive regulation of receptor internalization / chromosome, centromeric region / glial cell projection / mRNA transport / Cajal body / mRNA export from nucleus / cell projection / negative regulation of cytoplasmic translation / regulation of mRNA stability / translation regulator activity / translation repressor activity / negative regulation of translational initiation / signaling adaptor activity / translation initiation factor binding / RNA splicing / excitatory synapse / axon terminus / stress granule assembly / positive regulation of translation / cellular response to virus / mRNA 3'-UTR binding / molecular condensate scaffold activity / RNA stem-loop binding / mRNA 5'-UTR binding / cytoplasmic ribonucleoprotein granule / mRNA processing / cytoplasmic stress granule / nervous system development / presynapse / chromosome / growth cone / ribosome binding / presynaptic membrane / G-quadruplex RNA binding / microtubule binding / dendritic spine / perikaryon / transmembrane transporter binding / postsynaptic membrane / postsynapse / postsynaptic density / neuron projection / negative regulation of translation / protein heterodimerization activity / ribonucleoprotein complex / axon / DNA repair / mRNA binding / chromatin binding / nucleolus / dendrite / synapse / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / : / : / : / : / Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core / Fragile X messenger ribonucleoprotein 1 / Synaptic functional regulator FMRP, KH0 domain / FMR1, tudor domain ...Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / : / : / : / : / Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core / Fragile X messenger ribonucleoprotein 1 / Synaptic functional regulator FMRP, KH0 domain / FMR1, tudor domain / Fragile X-related 1 protein core C terminal / FMRP KH0 domain / Fragile X messenger ribonucleoprotein 1, Tudor domain / Agenet-like domain profile. / Agenet-like domain / Agenet domain / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain
Similarity search - Domain/homology
RNA / RNA (> 10) / Fragile X messenger ribonucleoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsPhan, A. / Kuryavyi, V. / Darnell, J. / Serganov, A. / Majumdar, A. / Ilin, S. / Darnell, R. / Patel, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction.
Authors: 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.
History
DepositionMar 3, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (36-MER)
B: Fragile X mental retardation 1 protein


Theoretical massNumber of molelcules
Total (without water)13,5632
Polymers13,5632
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (36-MER)


Mass: 11805.026 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein/peptide Fragile X mental retardation 1 protein / FMRP / Protein FMR-1


Mass: 1757.924 Da / Num. of mol.: 1 / Fragment: RNA-binding RGG-box residues 527-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FMR1 / References: UniProt: Q06787

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111JR
1212D 1H-1H NOESY
1312D 1H-1H COSY
1412D 1H-1H TOCSY
1522D 1H-13C HSQC
1622D 1H-15N HSQC
1722D 13C-1H CTHSQC
182HNH-COSY
192HNN-COSY
1102(H)CCH-COSY
1112(H)CCH-TOCSY
112213C-edited NOESY
113215N-edited NOESY
114315N-1H HSQC
115313C-1H HSQC
1163HNCA
1173HNCO
1183HN(CO)CA
1193HN(CA)CB
1203HBHA(CO)NH
1213(H)CCH-TOCSY
1223(H)CCH-COSY
123313C-edited NOESY
124315N-edited NOESY
1254HNN-COSY
126413C-edited NOESY
127415N-edited NOESY
1285CTHSQC
1295(H)CCH-COSY
1305(H)CCH-TOCSY
131513C-edited NOESY
1326CTHSQC
1336(H)CCH-COSY
1346(H)CCH-TOCSY
135613C-edited NOESY
1367CTHSQC
1377(H)CCH-COSY
1387(H)CCH-TOCSY
139713C-edited NOESY
1408CTHSQC
1418(H)CCH-COSY
1428(H)CCH-TOCSY
143813C-edited NOESY
14491D 15N-filtered
14592D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM RNA (36-MER), 1 mM Peptide, 90% H2O/10% D2O and 100%D2O90% H2O/10% D2O and 100%D2O
20.5 mM [U-100% 13C; U-100% 15N] RNA (36-MER), 0.5 mM Peptide, 90% H2O/10% D2O and 100%D2O90% H2O/10% D2O and 100%D2O
30.5 mM RNA (36-MER), 0.5 mM [U-100% 13C; U-100% 15N] Peptide, 90% H2O/10% D2O and 100%D2O90% H2O/10% D2O and 100%D2O
40.2-0.5 mM [U-100% 13C; U-100% 15N] RNA (36-MER), 0.2-0.5 mM [U-100% 13C; U-100% 15N] Peptide, 90% H2O/10% D2O and 100%D2O90% H2O/10% D2O and 100%D2O
50.5 mM [U-13C; U-15N]-Gua RNA (36-MER), 0.5 mM Peptide, 90% H2O/10% D2O and 100%D2O90% H2O/10% D2O and 100%D2O
60.2 mM [U-13C; U-15N]-Ade RNA (36-MER), 0.2 mM Peptide, 90% H2O/10% D2O and 100%D2O90% H2O/10% D2O and 100%D2O
70.2 mM [U-13C; U-15N]-Cyt RNA (36-MER), 0.2 mM Peptide, 90% H2O/10% D2O and 100%D2O90% H2O/10% D2O and 100%D2O
80.2 mM [U-13C; U-15N]-Ura RNA (36-MER), 0.2 mM Peptide, 90% H2O/10% D2O and 100%D2O90% H2O/10% D2O and 100%D2O
90.2 mM rG-to-dG and rU-to-dU 2% 15N-labelled RNA (36-MER), 0.2 mM Peptide, 90% H2O/10% D2O and 100%D2O90% H2O/10% D2O and 100%D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
1 mMRNA (36-MER)-11
1 mMPeptide-21
0.5 mMRNA (36-MER)-3[U-100% 13C; U-100% 15N]2
0.5 mMPeptide-42
0.5 mMRNA (36-MER)-53
0.5 mMPeptide-6[U-100% 13C; U-100% 15N]3
mMRNA (36-MER)-7[U-100% 13C; U-100% 15N]0.2-0.54
mMPeptide-8[U-100% 13C; U-100% 15N]0.2-0.54
0.5 mMRNA (36-MER)-9[U-13C; U-15N]-Gua5
0.5 mMPeptide-105
0.2 mMRNA (36-MER)-11[U-13C; U-15N]-Ade6
0.2 mMPeptide-126
0.2 mMRNA (36-MER)-13[U-13C; U-15N]-Cyt7
0.2 mMPeptide-147
0.2 mMRNA (36-MER)-15[U-13C; U-15N]-Ura8
0.2 mMPeptide-168
0.2 mMRNA (36-MER)-17rG-to-dG and rU-to-dU 2% 15N-labelled9
0.2 mMPeptide-189
Sample conditionsIonic strength: 0.05 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE8004

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
AmberAccelrys Software Inc.geometry optimization
FelixAccelrys Software Inc.processing
VNMRVariancollection
TopSpinBruker Biospincollection
CARAK. Wuthrichdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
AmberAccelrys Software Inc.refinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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