[English] 日本語
Yorodumi
- PDB-2la5: RNA Duplex-Quadruplex Junction Complex with FMRP RGG peptide -

+
Open data


ID or keywords:

Loading...

-
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 translation at presynapse, modulating synaptic transmission / modulation by host of viral RNA genome replication / regulation of neuronal action potential / growth cone filopodium / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / negative regulation of long-term synaptic depression / neuronal ribonucleoprotein granule ...positive regulation of intracellular transport of viral material / regulation of translation at presynapse, modulating synaptic transmission / modulation by host of viral RNA genome replication / regulation of neuronal action potential / growth cone filopodium / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / negative regulation of long-term synaptic depression / neuronal ribonucleoprotein granule / animal organ development / negative regulation of voltage-gated calcium channel activity / dendritic filopodium / RNA strand annealing activity / chromocenter / regulation of dendritic spine development / positive regulation of long-term neuronal synaptic plasticity / filopodium tip / regulation of neurotransmitter secretion / negative regulation of synaptic vesicle exocytosis / regulation of filopodium assembly / non-membrane-bounded organelle assembly / positive regulation of proteasomal protein catabolic process / N6-methyladenosine-containing RNA reader activity / siRNA binding / poly(A) binding / regulatory ncRNA-mediated gene silencing / glutamate receptor signaling pathway / sequence-specific mRNA binding / poly(U) RNA binding / miRNA binding / positive regulation of filopodium assembly / intracellular non-membrane-bounded organelle / regulation of alternative mRNA splicing, via spliceosome / dynein complex binding / positive regulation of dendritic spine development / positive regulation of receptor internalization / glial cell projection / chromosome, centromeric region / mRNA transport / negative regulation of cytoplasmic translation / mRNA export from nucleus / translation regulator activity / Cajal body / signaling adaptor activity / axon terminus / stress granule assembly / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / regulation of mRNA stability / methylated histone binding / RNA splicing / molecular condensate scaffold activity / cell projection / mRNA 3'-UTR binding / positive regulation of translation / cellular response to virus / mRNA 5'-UTR binding / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / mRNA processing / RNA stem-loop binding / ribosome binding / presynapse / chromosome / nervous system development / presynaptic membrane / growth cone / G-quadruplex RNA binding / microtubule binding / postsynaptic membrane / perikaryon / transmembrane transporter binding / postsynapse / dendritic spine / postsynaptic density / negative regulation of translation / neuron projection / ribonucleoprotein complex / protein heterodimerization activity / axon / DNA repair / mRNA binding / synapse / dendrite / chromatin binding / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / membrane / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more