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- PDB-7ymf: Crystal Structure of DDX3X449_450ET>DP -

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Basic information

Entry
Database: PDB / ID: 7ymf
TitleCrystal Structure of DDX3X449_450ET>DP
Components(ATP-dependent RNA helicase DDX3X) x 2
KeywordsHYDROLASE / DDX3X / NUCLEAR PROTEIN
Function / homology
Function and homology information


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 / gamete generation / positive regulation of mitochondrial translation ...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 / gamete generation / positive regulation of mitochondrial translation / positive regulation of protein K63-linked ubiquitination / NLRP3 inflammasome complex / cellular response to arsenic-containing substance / poly(A) binding / gamma-tubulin binding / P granule / cellular response to osmotic stress / negative regulation of non-canonical NF-kappaB signal transduction / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / transcription factor binding / lipid homeostasis / cell leading edge / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of interferon-alpha production / positive regulation of translational initiation / ribosomal small subunit binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of type I interferon production / positive regulation of G1/S transition of mitotic cell cycle / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / DNA helicase activity / translation initiation factor binding / signaling adaptor activity / stress granule assembly / intrinsic apoptotic signaling pathway / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / protein serine/threonine kinase activator activity / cytosolic ribosome assembly / positive regulation of translation / chromosome segregation / translational initiation / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of cell growth / response to virus / cellular response to virus / Wnt signaling pathway / mRNA 5'-UTR binding / RNA stem-loop binding / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / lamellipodium / positive regulation of cell growth / secretory granule lumen / ficolin-1-rich granule lumen / cell differentiation / RNA helicase activity / negative regulation of translation / intracellular signal transduction / RNA helicase / cadherin binding / positive regulation of apoptotic process / innate immune response / negative regulation of gene expression / GTPase activity / mRNA binding / centrosome / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / 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 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-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 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
Similarity search - Domain/homology
ATP-dependent RNA helicase DDX3X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXiong, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal Structure of DDX3X449_450ET>DP
Authors: Xiong, J.
History
DepositionJul 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)54,4432
Polymers54,4432
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.560, 106.560, 116.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein ATP-dependent RNA helicase DDX3X


Mass: 34187.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX3X / Production host: Escherichia coli (E. coli) / References: UniProt: O00571, RNA helicase
#2: Protein ATP-dependent RNA helicase DDX3X


Mass: 20255.672 Da / Num. of mol.: 1 / Mutation: E449D, T450P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX3X / Production host: Escherichia coli (E. coli) / References: UniProt: O00571, RNA helicase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.5, 1.5 M Sodium Formate , 50 mM Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 21930 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 27.52 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.039 / Net I/σ(I): 24.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 2050 / CC1/2: 0.92 / Rpim(I) all: 0.264 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PXA

4pxa


Resolution: 2.3→49.32 Å / SU ML: 0.2455 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 25.378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244 1097 5.01 %
Rwork0.1852 20820 -
obs0.1881 21917 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 0 189 3497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01213403
X-RAY DIFFRACTIONf_angle_d1.37514605
X-RAY DIFFRACTIONf_chiral_restr0.0796509
X-RAY DIFFRACTIONf_plane_restr0.0081605
X-RAY DIFFRACTIONf_dihedral_angle_d21.67961293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.26781330.21722559X-RAY DIFFRACTION97.78
2.4-2.530.26731430.19752620X-RAY DIFFRACTION99.96
2.53-2.690.27061560.21622602X-RAY DIFFRACTION100
2.69-2.90.27771270.20342579X-RAY DIFFRACTION100
2.9-3.190.29481330.2052614X-RAY DIFFRACTION100
3.19-3.650.2281240.17472630X-RAY DIFFRACTION100
3.65-4.590.19241410.16112619X-RAY DIFFRACTION100
4.6-49.320.24111400.17572597X-RAY DIFFRACTION99.89

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