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- PDB-6zbk: Crystal structure of the human complex between RPAP3 and TRBP -

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Basic information

Entry
Database: PDB / ID: 6zbk
TitleCrystal structure of the human complex between RPAP3 and TRBP
Components
  • RISC-loading complex subunit TARBP2
  • RNA polymerase II-associated protein 3
KeywordsRNA BINDING PROTEIN / RNPs / MicroRNAs / RNA Induced Silencing Complex / dsRNA pathways
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 / global gene silencing by mRNA cleavage / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / R2TP 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 / global gene silencing by mRNA cleavage / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / R2TP complex / RISC-loading complex / RPAP3/R2TP/prefoldin-like complex / RISC complex assembly / miRNA processing / pre-miRNA processing / siRNA processing / siRNA binding / RISC complex / pre-mRNA binding / protein folding chaperone complex / miRNA binding / MicroRNA (miRNA) biogenesis / 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 / protein stabilization / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif ...: / 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 / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Tetratricopeptide repeat / Tetratricopeptide repeat / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
RISC-loading complex subunit TARBP2 / RNA polymerase II-associated protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å
AuthorsCharron, C. / Abel, Y. / Charpentier, B. / Rederstorff, M.
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: The interaction between RPAP3 and TRBP reveals a possible involvement of the HSP90/R2TP chaperone complex in the regulation of miRNA activity.
Authors: Abel, Y. / Charron, C. / Virciglio, C. / Bourguignon-Igel, V. / Quinternet, M. / Chagot, M.E. / Robert, M.C. / Verheggen, C. / Branlant, C. / Bertrand, E. / Manival, X. / Charpentier, B. / Rederstorff, M.
History
DepositionJun 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase II-associated protein 3
B: RISC-loading complex subunit TARBP2


Theoretical massNumber of molelcules
Total (without water)25,6642
Polymers25,6642
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-9 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.770, 158.130, 32.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

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Components

#1: Protein RNA polymerase II-associated protein 3


Mass: 14066.897 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPAP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H6T3
#2: Protein RISC-loading complex subunit TARBP2 / TAR RNA-binding protein 2 / Trans-activation-responsive RNA-binding protein


Mass: 11597.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TARBP2, TRBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q15633
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 3,350 and TacsimateTM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.49→39.53 Å / Num. obs: 34245 / % possible obs: 99 % / Redundancy: 6.2 % / Rsym value: 0.059 / Net I/σ(I): 18.6
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 5.1 / Num. unique obs: 5166 / Rsym value: 0.279 / % possible all: 94.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CGV,4WYQ

4cgv

4wyq


Resolution: 1.49→39.53 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.407 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 1353 4.1 %RANDOM
Rwork0.1775 ---
obs0.1789 31848 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.03 Å2 / Biso mean: 16.14 Å2 / Biso min: 6.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.49→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 0 243 1944
Biso mean---26.46 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191725
X-RAY DIFFRACTIONr_bond_other_d0.0010.021665
X-RAY DIFFRACTIONr_angle_refined_deg2.0541.9812322
X-RAY DIFFRACTIONr_angle_other_deg0.9433832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4035218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30123.63677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08715312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2251515
X-RAY DIFFRACTIONr_chiral_restr0.1250.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
LS refinement shellResolution: 1.494→1.533 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 75 -
Rwork0.281 2085 -
all-2160 -
obs--85.71 %

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