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Basic information

Entry
Database: PDB / ID: 3vyy
TitleStructural insights into RISC assembly facilitated by dsRNA binding domains of human RNA helicase A (DHX9)
Components
  • ATP-dependent RNA helicase A
  • RNA (5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')
KeywordsHYDROLASE/RNA / dsRBD-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 / regulation of cytoplasmic translation / regulatory region RNA binding / positive regulation of RNA export from nucleus / DNA-templated viral transcription / positive regulation of viral transcription / triplex DNA binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity ...single-stranded 3'-5' DNA helicase activity / 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 / DNA-templated viral transcription / positive regulation of viral transcription / triplex DNA binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / RISC complex binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule / G-quadruplex DNA unwinding / nucleoside triphosphate diphosphatase activity / nuclear stress granule / positive regulation of interleukin-18 production / perichromatin fibrils / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / 3'-5' RNA helicase activity / alternative mRNA splicing, via spliceosome / RNA secondary structure unwinding / RISC-loading complex / miRNA-mediated post-transcriptional gene silencing / RISC complex assembly / regulation of mRNA processing / regulation of defense response to virus by host / importin-alpha family protein binding / RIP-mediated NFkB activation via ZBP1 / positive regulation of response to cytokine stimulus / siRNA binding / positive regulation of cytoplasmic translation / positive regulation of innate immune response / RISC complex / sequence-specific mRNA binding / RNA polymerase binding / DNA duplex unwinding / 3'-5' DNA helicase activity / cellular response to exogenous dsRNA / pyroptotic inflammatory response / RNA polymerase II complex binding / DNA replication origin binding / positive regulation of interferon-alpha production / mRNA transport / positive regulation of interferon-beta production / DNA helicase activity / positive regulation of DNA repair / 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 / positive regulation of inflammatory response / cytoplasmic ribonucleoprotein granule / positive regulation of interleukin-6 production / osteoblast differentiation / RNA stem-loop binding / positive regulation of tumor necrosis factor production / double-stranded RNA binding / positive regulation of fibroblast proliferation / actin cytoskeleton / rhythmic process / ribosome binding / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / single-stranded DNA binding / double-stranded DNA binding / protein-containing complex assembly / 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 / 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 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.1Dec 4, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn / reflns / reflns_shell
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _reflns.pdbx_Rsym_value / _reflns.pdbx_netI_over_sigmaI / _reflns_shell.meanI_over_sigI_obs
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2
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
Revision 1.3Nov 8, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,6027
Polymers36,6027
Non-polymers00
Water00
1
A: ATP-dependent RNA helicase A
C: RNA (5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')
D: RNA (5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,6983
Polymers16,6983
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-14 kcal/mol
Surface area9030 Å2
MethodPISA
2
B: ATP-dependent RNA helicase A
E: RNA (5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')
F: RNA (5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,6983
Polymers16,6983
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-12 kcal/mol
Surface area8940 Å2
MethodPISA
3
G: RNA (5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')

G: RNA (5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,4142
Polymers6,4142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area930 Å2
ΔGint-2 kcal/mol
Surface area3810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.252, 78.529, 112.242
Angle α, β, γ (deg.)90.00, 98.81, 90.00
Int Tables number5
Space group name H-MC121

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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: 10283.698 Da / Num. of mol.: 2 / Fragment: UNP residues 1-91
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(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')


Mass: 3206.980 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: The sequence is synthesized in vitro. / Source: (synth.) synthetic construct (others)

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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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, CaAc2, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.007 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 9520 / Num. obs: 9511 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rsym value: 0.086 / Net I/σ(I): 27.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 5.8 / Rsym value: 0.254 / % possible all: 94.7

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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: 1WHQ

1whq


Resolution: 2.9→37.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.895 / SU B: 37.4 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26175 481 4.8 %RANDOM
Rwork0.2189 ---
obs0.22097 9511 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.391 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å21.99 Å2
2---1.37 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.9→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 1060 0 0 2416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212560
X-RAY DIFFRACTIONr_angle_refined_deg1.6442.4653684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.12624.44472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.95315251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3551510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021587
X-RAY DIFFRACTIONr_nbd_refined0.2280.21136
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21683
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.293
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.28
X-RAY DIFFRACTIONr_mcbond_it0.6841.5858
X-RAY DIFFRACTIONr_mcangle_it1.16221338
X-RAY DIFFRACTIONr_scbond_it1.10732327
X-RAY DIFFRACTIONr_scangle_it1.8654.52346
LS refinement shellResolution: 2.896→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 31 -
Rwork0.272 640 -
obs--91.92 %
Refinement TLS params.Method: refined / Origin x: 13.7114 Å / Origin y: -0.0798 Å / Origin z: 33.3669 Å
111213212223313233
T-0.1089 Å2-0.1049 Å2-0.0556 Å2-0.0283 Å2-0.0684 Å2---0.1063 Å2
L2.6999 °20.893 °2-1.9679 °2-2.8676 °2-0.5238 °2--2.087 °2
S-0.1013 Å °0.5609 Å °-0.0216 Å °-0.5681 Å °0.1681 Å °-0.1574 Å °-0.1374 Å °-0.2803 Å °-0.0668 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 86
2X-RAY DIFFRACTION1B1 - 84
3X-RAY DIFFRACTION1C1 - 10
4X-RAY DIFFRACTION1D1 - 10
5X-RAY DIFFRACTION1E1 - 10
6X-RAY DIFFRACTION1F1 - 10
7X-RAY DIFFRACTION1G1 - 10

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