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- PDB-5n8m: Structure of TRBP dsRBD 1 and 2 in complex with a 19 bp siRNA (Co... -

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Basic information

Entry
Database: PDB / ID: 5n8m
TitleStructure of TRBP dsRBD 1 and 2 in complex with a 19 bp siRNA (Complex A)
Components
  • RISC-loading complex subunit TARBP2
  • RNA (5'-R(*GP*UP*AP*CP*GP*GP*AP*AP*UP*AP*GP*AP*UP*AP*AP*UP*UP*AP*AP*UP*U)-3')
  • RNA (5'-R(*UP*UP*AP*AP*UP*UP*AP*UP*CP*UP*AP*UP*UP*CP*CP*GP*UP*AP*CP*UP*U)-3')
KeywordsRNA BINDING PROTEIN / TRBP / siRNA / protein-RNA complex / RNAi
Function / homology
Function and homology information


regulation of siRNA processing / regulation of miRNA processing / regulation of viral transcription / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / regulation of regulatory ncRNA processing / negative regulation of defense response to virus by host / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / global gene silencing by mRNA cleavage / RISC-loading complex ...regulation of siRNA processing / regulation of miRNA processing / regulation of viral transcription / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / regulation of regulatory ncRNA processing / negative regulation of defense response to virus by host / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / global gene silencing by mRNA cleavage / RISC-loading complex / RISC complex assembly / miRNA processing / siRNA binding / pre-miRNA processing / pre-mRNA binding / siRNA processing / RISC complex / MicroRNA (miRNA) biogenesis / miRNA binding / positive regulation of viral genome replication / protein sequestering activity / negative regulation of protein kinase activity / PKR-mediated signaling / double-stranded RNA binding / regulation of translation / nuclear body / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RISC-loading complex subunit TRBP2 / TRBP2 , first double-stranded RNA binding domain / TRBP2 , second double-stranded RNA binding domain / TRBP2 , third double-stranded RNA binding domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain ...RISC-loading complex subunit TRBP2 / TRBP2 , first double-stranded RNA binding domain / TRBP2 , second double-stranded RNA binding domain / TRBP2 , third double-stranded RNA binding domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RISC-loading complex subunit TARBP2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsMasliah, G. / Maris, C. / Allain, H.-T.F.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
CTI11329.1 PFLS-LS Switzerland
SinergiaCRSII5_170976 Switzerland
NCCR RNA and Disease Switzerland
CitationJournal: EMBO J. / Year: 2018
Title: Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains.
Authors: Masliah, G. / Maris, C. / Konig, S.L. / Yulikov, M. / Aeschimann, F. / Malinowska, A.L. / Mabille, J. / Weiler, J. / Holla, A. / Hunziker, J. / Meisner-Kober, N. / Schuler, B. / Jeschke, G. / Allain, F.H.
History
DepositionFeb 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 28, 2018Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RISC-loading complex subunit TARBP2
B: RNA (5'-R(*UP*UP*AP*AP*UP*UP*AP*UP*CP*UP*AP*UP*UP*CP*CP*GP*UP*AP*CP*UP*U)-3')
C: RNA (5'-R(*GP*UP*AP*CP*GP*GP*AP*AP*UP*AP*GP*AP*UP*AP*AP*UP*UP*AP*AP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)36,2943
Polymers36,2943
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5070 Å2
ΔGint-30 kcal/mol
Surface area14730 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein RISC-loading complex subunit TARBP2 / TAR RNA-binding protein 2 / Trans-activation-responsive RNA-binding protein


Mass: 23012.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: huTRBP N-terminal dsRBD1 and 2 (residues 16 to 227)
Source: (gene. exp.) Homo sapiens (human) / Gene: TARBP2, TRBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q15633
#2: RNA chain RNA (5'-R(*UP*UP*AP*AP*UP*UP*AP*UP*CP*UP*AP*UP*UP*CP*CP*GP*UP*AP*CP*UP*U)-3')


Mass: 6534.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*GP*UP*AP*CP*GP*GP*AP*AP*UP*AP*GP*AP*UP*AP*AP*UP*UP*AP*AP*UP*U)-3')


Mass: 6747.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic43D CBCA(CO)NH
131isotropic1(H)CC(CO)NH
141isotropic23D 1H-13C NOESY aliphatic
151isotropic23D 1H-15N NOESY
162isotropic33D (H)CCH-TOCSY
172isotropic23D 1H-13C NOESY aliphatic
182isotropic23D 1H-15N NOESY
192isotropic13D HNCA
1123isotropic43D f1-13C-filtered, f2-13C-edited NOESY aliphatic-HMQC
1114isotropic1TROSY IPAP
1105anisotropic1TROSY IPAP

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 13C; U-100% 15N; U-80% 2H] dsRBD1, 1 mM EL86, 90% H2O/10% D2O15N_13C_RBD1-EL8690% H2O/10% D2O
solution21 mM [U-100% 13C; U-100% 15N] dsRBD2, 1 mM EL86, 90% H2O/10% D2O15N_13C_RBD2-EL8690% H2O/10% D2O
solution31 mM [U-100% 13C; U-100% 15N; U-80% 2H] dsRBD12, 1 mM EL86, 100% D2O15N_13C_2H_RBD12-EL86_d2o100% D2O
solution41 mM [U-100% 13C; U-100% 15N; U-80% 2H] dsRBD12, 1 mM EL86, 90% H2O/10% D2O15N_13C_2H_RBD12-EL86_iso90% H2O/10% D2O
filamentous virus51 mM [U-100% 13C; U-100% 15N; U-80% 2H] dsRBD12, 1 mM EL86, 90% H2O/10% D2O15N_13C_2H_RBD12-EL86_ani90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMdsRBD1[U-100% 13C; U-100% 15N; U-80% 2H]1
1 mMEL86natural abundance1
1 mMdsRBD2[U-100% 13C; U-100% 15N]2
1 mMEL86natural abundance2
1 mMdsRBD12[U-100% 13C; U-100% 15N; U-80% 2H]3
1 mMEL86natural abundance3
1 mMdsRBD12[U-100% 13C; U-100% 15N; U-80% 2H]4
1 mMEL86natural abundance4
1 mMdsRBD12[U-100% 13C; U-100% 15N; U-80% 2H]5
1 mMEL86natural abundance5
Sample conditionsIonic strength: 20 mM / Ionic strength err: 0.2 / Label: conditions_1 / pH: 6.5 / Pressure: AMBIENT atm / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7501
Bruker AVANCE IIIBrukerAVANCE III9002
Bruker AVANCE IIIBrukerAVANCE III6004
Bruker AVANCE IIIBrukerAVANCE III5003

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Processing

NMR software
NameVersionDeveloperClassification
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
TopSpin3Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 20

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