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- PDB-4px9: DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop -

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Basic information

Entry
Database: PDB / ID: 4px9
TitleDEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop
ComponentsATP-dependent RNA helicase DDX3X
KeywordsTRANSLATION / RNA BINDING PROTEIN / DEAD-box helicase / HYDROLASE
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 / positive regulation of chemokine (C-C motif) ligand 5 production / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / 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 / positive regulation of chemokine (C-C motif) ligand 5 production / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / 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 / P granule / RNA stem-loop binding / gamma-tubulin binding / cellular response to osmotic stress / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of NLRP3 inflammasome complex assembly / cell leading edge / lipid homeostasis / positive regulation of interferon-alpha production / ribosomal small subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of translational initiation / transcription factor 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 / positive regulation of viral genome replication / negative regulation of protein-containing complex assembly / negative regulation of intrinsic apoptotic signaling pathway / signaling adaptor activity / stress granule assembly / translation initiation factor binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / translational initiation / positive regulation of protein autophosphorylation / DNA helicase activity / protein serine/threonine kinase activator activity / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / intrinsic apoptotic signaling pathway / cytosolic ribosome assembly / positive regulation of translation / chromosome segregation / response to virus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / mRNA 5'-UTR binding / positive regulation of protein serine/threonine kinase activity / negative regulation of cell growth / Wnt signaling pathway / cellular response to virus / 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 / negative regulation of translation / RNA helicase activity / cell differentiation / RNA helicase / intracellular signal transduction / cadherin binding / positive regulation of apoptotic process / innate immune response / mRNA binding / GTPase activity / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent RNA helicase DDX3X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsEpling, L.B. / Grace, C.R. / Lowe, B.R. / Partridge, J.F. / Enemark, E.J.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Cancer-Associated Mutants of RNA Helicase DDX3X Are Defective in RNA-Stimulated ATP Hydrolysis.
Authors: Epling, L.B. / Grace, C.R. / Lowe, B.R. / Partridge, J.F. / Enemark, E.J.
History
DepositionMar 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DDX3X
B: ATP-dependent RNA helicase DDX3X
C: ATP-dependent RNA helicase DDX3X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3476
Polymers99,0663
Non-polymers1,2823
Water0
1
A: ATP-dependent RNA helicase DDX3X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4492
Polymers33,0221
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-dependent RNA helicase DDX3X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4492
Polymers33,0221
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ATP-dependent RNA helicase DDX3X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4492
Polymers33,0221
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.637, 75.637, 121.388
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: 33021.934 Da / Num. of mol.: 3 / Fragment: UNP residues 135-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DBX, DDX3, DDX3X / Plasmid: pLE231 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: O00571, RNA helicase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 50 mM Hepes 7.6; 7% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 34297 / Num. obs: 34163 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 26.95
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.28 / Num. unique all: 3458 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I4I

2i4i


Resolution: 2.31→36.11 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1794086.67 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1755 5.1 %RANDOM
Rwork0.255 ---
obs0.255 34116 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1571 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 71.1 Å2
Baniso -1Baniso -2Baniso -3
1-12.76 Å20 Å20 Å2
2--12.76 Å20 Å2
3----25.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.31→36.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6265 0 81 0 6346
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.31→2.38 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.426 160 5 %
Rwork0.386 3061 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6adp.paramadp.top

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