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- PDB-6o5f: Crystal structure of DEAD-box RNA helicase DDX3X at pre-unwound state -

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Basic information

Entry
Database: PDB / ID: 6o5f
TitleCrystal structure of DEAD-box RNA helicase DDX3X at pre-unwound state
Components
  • ATP-dependent RNA helicase DDX3X
  • RNA (5'-R(P*CP*AP*AP*GP*GP*UP*CP*AP*UP*UP*CP*GP*CP*AP*AP*GP*AP*GP*UP*GP*GP*CP*C)-3')
KeywordsHYDROLASE/RNA / DDX3X / DEAD-box / RNA helicase / HYDROLASE / HYDROLASE-RNA complex
Function / homology
Function and homology information


positive regulation of protein acetylation / CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / RNA secondary structure unwinding ...positive regulation of protein acetylation / CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / RNA secondary structure unwinding / gamete generation / NLRP3 inflammasome complex / positive regulation of protein K63-linked ubiquitination / cellular response to arsenic-containing substance / poly(A) binding / gamma-tubulin binding / cellular response to osmotic stress / P granule / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of NLRP3 inflammasome complex assembly / cell leading edge / lipid homeostasis / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / transcription factor binding / ribosomal small subunit binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of interferon-alpha production / positive regulation of type I interferon production / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of translational initiation / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / signaling adaptor activity / negative regulation of intrinsic apoptotic signaling pathway / stress granule assembly / RNA stem-loop binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of protein autophosphorylation / translational initiation / translation initiation factor binding / DNA helicase activity / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / protein serine/threonine kinase activator activity / intrinsic apoptotic signaling pathway / cytosolic ribosome assembly / chromosome segregation / positive regulation of translation / response to virus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein serine/threonine kinase activity / negative regulation of cell growth / cellular response to virus / Wnt signaling pathway / mRNA 5'-UTR binding / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / lamellipodium / positive regulation of cell growth / secretory granule lumen / ficolin-1-rich granule lumen / RNA helicase activity / negative regulation of translation / cell differentiation / intracellular signal transduction / RNA helicase / cadherin binding / positive regulation of apoptotic process / negative regulation of gene expression / innate immune response / GTPase activity / mRNA binding / centrosome / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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
Similarity search - Domain/homology
RNA / RNA (> 10) / ATP-dependent RNA helicase DDX3X
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.504 Å
AuthorsSong, H. / Ji, X.
CitationJournal: Nat Commun / Year: 2019
Title: The mechanism of RNA duplex recognition and unwinding by DEAD-box helicase DDX3X.
Authors: Song, H. / Ji, X.
History
DepositionMar 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DDX3X
B: ATP-dependent RNA helicase DDX3X
C: RNA (5'-R(P*CP*AP*AP*GP*GP*UP*CP*AP*UP*UP*CP*GP*CP*AP*AP*GP*AP*GP*UP*GP*GP*CP*C)-3')
D: RNA (5'-R(P*CP*AP*AP*GP*GP*UP*CP*AP*UP*UP*CP*GP*CP*AP*AP*GP*AP*GP*UP*GP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,67311
Polymers125,4244
Non-polymers2487
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, The crystal structure is validated by SAXS experiment
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-91 kcal/mol
Surface area44720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.102, 66.102, 230.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein ATP-dependent RNA helicase DDX3X / DEAD box protein 3 / X-chromosomal / DEAD box / X isoform / Helicase-like protein 2 / HLP2


Mass: 53701.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX3X, DBX, DDX3 / Production host: Escherichia coli (E. coli) / References: UniProt: O00571, RNA helicase
#2: RNA chain RNA (5'-R(P*CP*AP*AP*GP*GP*UP*CP*AP*UP*UP*CP*GP*CP*AP*AP*GP*AP*GP*UP*GP*GP*CP*C)-3')


Mass: 9010.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25% (v/v) PEG 3350, 0.2 M magnesium chloride, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 37345 / % possible obs: 96.4 % / Redundancy: 3.8 % / Rpim(I) all: 0.092 / Net I/σ(I): 8.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Mean I/σ(I) obs: 0.9 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E7I

5e7i


Resolution: 2.504→35.902 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 28.89
RfactorNum. reflection% reflection
Rfree0.2461 1010 2.7 %
Rwork0.2117 --
obs0.2127 37345 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.504→35.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 1006 7 72 7745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047913
X-RAY DIFFRACTIONf_angle_d0.710918
X-RAY DIFFRACTIONf_dihedral_angle_d21.1683142
X-RAY DIFFRACTIONf_chiral_restr0.0461249
X-RAY DIFFRACTIONf_plane_restr0.0041243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5037-2.63560.35271500.30085314X-RAY DIFFRACTION98
2.6356-2.80070.29311490.27155274X-RAY DIFFRACTION98
2.8007-3.01690.33331430.25525370X-RAY DIFFRACTION99
3.0169-3.32030.32281430.23295261X-RAY DIFFRACTION98
3.3203-3.80030.23561540.20445192X-RAY DIFFRACTION96
3.8003-4.78610.21661360.17674924X-RAY DIFFRACTION92
4.7861-35.90530.20381350.19975000X-RAY DIFFRACTION93

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