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- PDB-3vyx: Structural insights into RISC assembly facilitated by dsRNA bindi... -

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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


single-stranded 3'-5' DNA helicase activity / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulatory region RNA binding / regulation of cytoplasmic translation / positive regulation of RNA export from nucleus / positive regulation of viral transcription / DNA-templated viral transcription / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / RISC complex binding ...single-stranded 3'-5' DNA helicase activity / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulatory region RNA binding / regulation of cytoplasmic translation / positive regulation of RNA export from nucleus / positive regulation of viral transcription / DNA-templated viral transcription / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / RISC complex binding / positive regulation of interleukin-18 production / triplex DNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule / nucleoside triphosphate diphosphatase activity / G-quadruplex DNA unwinding / perichromatin fibrils / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / alternative mRNA splicing, via spliceosome / nuclear stress granule / RNA secondary structure unwinding / 3'-5' RNA helicase activity / RISC-loading complex / miRNA-mediated post-transcriptional gene silencing / RISC complex assembly / regulation of mRNA processing / regulation of defense response to virus by host / RIP-mediated NFkB activation via ZBP1 / importin-alpha family protein binding / positive regulation of response to cytokine stimulus / positive regulation of cytoplasmic translation / siRNA binding / positive regulation of innate immune response / RISC complex / sequence-specific mRNA binding / RNA polymerase binding / cellular response to exogenous dsRNA / DNA duplex unwinding / 3'-5' DNA helicase activity / pyroptotic inflammatory response / RNA polymerase II complex binding / DNA replication origin binding / positive regulation of interferon-alpha production / mRNA transport / DNA helicase activity / positive regulation of interferon-beta production / positive regulation of DNA repair / mRNA Splicing - Major Pathway / ribonucleoside triphosphate phosphatase activity / positive regulation of DNA replication / promoter-specific chromatin binding / DNA-templated transcription termination / transcription coregulator activity / PKR-mediated signaling / chromatin DNA binding / positive regulation of inflammatory response / cytoplasmic ribonucleoprotein granule / positive regulation of interleukin-6 production / osteoblast differentiation / RNA stem-loop binding / positive regulation of fibroblast proliferation / positive regulation of tumor necrosis factor production / double-stranded RNA binding / rhythmic process / actin cytoskeleton / cellular response to tumor necrosis factor / ribosome binding / positive regulation of NF-kappaB transcription factor activity / single-stranded DNA binding / double-stranded DNA binding / protein-containing complex assembly / RNA polymerase II-specific DNA-binding transcription factor binding / DNA replication / RNA helicase activity / transcription coactivator activity / single-stranded RNA binding / nuclear body / RNA helicase / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / innate immune response / mRNA binding / centrosome / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm
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 (HA2), winged-helix / Helicase-associated domain / 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 (HA2), winged-helix / Helicase-associated domain / 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 domain / DEAD/DEAH box helicase / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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.

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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: 2.76 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

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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

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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

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