[English] 日本語
Yorodumi
- PDB-6zbk: Crystal structure of the human complex between RPAP3 and TRBP -

+
Open data


ID or keywords:

Loading...

-
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 / RPAP3/R2TP/prefoldin-like complex / RISC-loading complex / RISC complex assembly / miRNA processing / pre-miRNA processing / siRNA processing / siRNA binding / pre-mRNA binding / RISC complex / protein folding chaperone complex / MicroRNA (miRNA) biogenesis / miRNA binding / positive regulation of viral genome replication / protein sequestering activity / negative regulation of protein kinase activity / PKR-mediated signaling / regulation of translation / double-stranded RNA binding / protein stabilization / nuclear body / 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 / Tetratricopeptide repeat / Double-stranded RNA binding motif / Tetratricopeptide repeat 1 ...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 / Tetratricopeptide repeat / Double-stranded RNA binding motif / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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 %

+
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://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