[English] 日本語
Yorodumi
- PDB-3vyx: Structural insights into RISC assembly facilitated by dsRNA bindi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vyx
TitleStructural insights into RISC assembly facilitated by dsRNA binding domains of human RNA helicase (DHX9)
Components
  • ATP-dependent RNA helicase A
  • RNA (5'-R(P*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')
KeywordsHYDROLASE/RNA / protein-dsRNA complex / dsRBD fold / dsRNA binding / protein-protein interaction / HYDROLASE-RNA complex
Function / homology
Function and homology information


: / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulation of cytoplasmic translation / regulatory region RNA binding / positive regulation of RNA export from nucleus / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA-templated viral transcription / positive regulation of viral transcription / CRD-mediated mRNA stabilization ...: / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulation of cytoplasmic translation / regulatory region RNA binding / positive regulation of RNA export from nucleus / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA-templated viral transcription / positive regulation of viral transcription / CRD-mediated mRNA stabilization / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / triplex DNA binding / RISC complex binding / protein localization to cytoplasmic stress granule / nucleoside triphosphate diphosphatase activity / nuclear stress granule / G-quadruplex DNA unwinding / 3'-5' RNA helicase activity / perichromatin fibrils / positive regulation of interleukin-18 production / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / alternative mRNA splicing, via spliceosome / RNA secondary structure unwinding / RISC-loading complex / miRNA-mediated post-transcriptional gene silencing / regulation of mRNA processing / RISC complex assembly / positive regulation of cytoplasmic translation / single-stranded 3'-5' DNA helicase activity / regulation of defense response to virus by host / importin-alpha family protein binding / RIP-mediated NFkB activation via ZBP1 / siRNA binding / positive regulation of response to cytokine stimulus / positive regulation of innate immune response / sequence-specific mRNA binding / RISC complex / RNA polymerase binding / DNA duplex unwinding / cellular response to exogenous dsRNA / pyroptotic inflammatory response / RNA polymerase II complex binding / 3'-5' DNA helicase activity / DNA replication origin binding / mRNA transport / positive regulation of interferon-alpha production / DNA helicase activity / positive regulation of DNA repair / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / mRNA Splicing - Major Pathway / positive regulation of DNA replication / promoter-specific chromatin binding / DNA-templated transcription termination / transcription coregulator activity / PKR-mediated signaling / chromatin DNA binding / cytoplasmic ribonucleoprotein granule / positive regulation of inflammatory response / osteoblast differentiation / RNA stem-loop binding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / double-stranded RNA binding / positive regulation of fibroblast proliferation / rhythmic process / actin cytoskeleton / ribosome binding / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / single-stranded DNA binding / protein-containing complex assembly / double-stranded DNA binding / DNA replication / RNA polymerase II-specific DNA-binding transcription factor binding / RNA helicase activity / transcription coactivator activity / single-stranded RNA binding / nuclear body / RNA helicase / ribonucleoprotein complex / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / innate immune response / centrosome / mRNA binding / nucleolus / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation ...DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / ATP-dependent RNA helicase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsYuan, Y.A. / Fu, Q.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9).
Authors: Fu, Q. / Yuan, Y.A.
History
DepositionOct 5, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent RNA helicase A
B: RNA (5'-R(P*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')
C: RNA (5'-R(P*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)19,4913
Polymers19,4913
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-13 kcal/mol
Surface area9110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.198, 63.198, 107.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein ATP-dependent RNA helicase A / RHA / DEAH box protein 9 / Leukophysin / LKP / Nuclear DNA helicase II / NDH II


Mass: 13076.770 Da / Num. of mol.: 1 / Fragment: UNP residues 152-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX9, DDX9, LKP, NDH2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08211, RNA helicase
#2: RNA chain RNA (5'-R(P*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')


Mass: 3206.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence is synthesized in vitro.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O / Details: This sequence is synthesized in vitro.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, KNO3, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 9800 / Num. obs: 9800 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.8 % / Rsym value: 0.095
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 12.5 % / Rsym value: 0.322 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UIL

1uil


Resolution: 2.29→41.27 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.204 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26312 497 4.8 %RANDOM
Rwork0.1931 ---
obs0.19639 9800 99.87 %-
all-9800 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.826 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2--1.29 Å20 Å2
3----2.57 Å2
Refinement stepCycle: LAST / Resolution: 2.29→41.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms765 432 0 82 1279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211260
X-RAY DIFFRACTIONr_angle_refined_deg1.7152.3771796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.694594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24523.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33715140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.845156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02803
X-RAY DIFFRACTIONr_nbd_refined0.1910.2485
X-RAY DIFFRACTIONr_nbtor_refined0.2860.2835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.27
X-RAY DIFFRACTIONr_mcbond_it0.9591.5480
X-RAY DIFFRACTIONr_mcangle_it1.5242740
X-RAY DIFFRACTIONr_scbond_it1.93231042
X-RAY DIFFRACTIONr_scangle_it2.6984.51056
LS refinement shellResolution: 2.294→2.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 38 -
Rwork0.218 696 -
obs--99.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.98030.32370.98911.436-0.92496.3012-0.06840.06180.01720.38510.14060.1412-0.3765-0.1047-0.07220.02590.04670.0216-0.12440.0159-0.03338.1503-14.1253-12.1455
20.0044-0.00290.0980.587-0.12252.19910.23960.13810.1469-0.12330.20960.04580.414-0.5608-0.44920.0147-0.03370.01670.05820.1159-0.0226-1.1128-30.3301-5.1455
31.6699-0.7089-0.00561.9038-0.99351.9420.133-0.10630.1020.4210.22140.11250.1896-0.2084-0.3544-0.00040.06540.0748-0.00040.092-0.04350.1087-30.8968-2.0893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A169 - 263
2X-RAY DIFFRACTION2B1 - 10
3X-RAY DIFFRACTION3C1 - 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://pdbjlvh1.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