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- PDB-2jgn: DDX3 helicase domain -

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Basic information

Entry
Database: PDB / ID: 2jgn
TitleDDX3 helicase domain
ComponentsATP-DEPENDENT RNA HELICASE DDX3X
KeywordsHYDROLASE / PHOSPHORYLATION / NUCLEOTIDE-BINDING / HELICASE / RNA-BINDING / ATP-BINDING / DNA-BINDING / NUCLEAR PROTEIN / HOST-VIRUS INTERACTION
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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DDX3X
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsRodamilans, B. / Montoya, G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Expression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of the Ddx3 RNA Helicase Domain.
Authors: Rodamilans, B. / Montoya, G.
History
DepositionFeb 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3Dec 13, 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

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


Theoretical massNumber of molelcules
Total (without water)63,5183
Polymers63,5183
Non-polymers00
Water3,477193
1
A: ATP-DEPENDENT RNA HELICASE DDX3X


Theoretical massNumber of molelcules
Total (without water)21,1731
Polymers21,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-DEPENDENT RNA HELICASE DDX3X


Theoretical massNumber of molelcules
Total (without water)21,1731
Polymers21,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ATP-DEPENDENT RNA HELICASE DDX3X


Theoretical massNumber of molelcules
Total (without water)21,1731
Polymers21,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.438, 61.032, 89.111
Angle α, β, γ (deg.)90.00, 101.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-DEPENDENT RNA HELICASE DDX3X / DBX / DDX3


Mass: 21172.598 Da / Num. of mol.: 3 / Fragment: HELICASE DOMAIN, RESIDUES 408-579
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCOLD III / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O00571, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.04 Å3/Da / Density % sol: 34 % / Description: NONE
Crystal growDetails: RESERVOIR: 2M (NH4)2SO4, 0.1M IMIDAZOLE PH 6.4 PLUS 5MM SPERMINE TETRA-HCL PROTEIN: 10MM HEPES, 500MM (NH4)2SO4, PH 8.0.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Details: MIRROR
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→87 Å / Num. obs: 105982 / % possible obs: 93.2 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.03
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.53 / % possible all: 72.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DB3

2db3


Resolution: 1.91→34.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.522 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1704 5 %RANDOM
Rwork0.198 ---
obs0.201 32363 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.16 Å2
2---0.28 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.91→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 0 193 3920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223781
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9515104
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62524.541185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06915670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5171524
X-RAY DIFFRACTIONr_chiral_restr0.1190.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022805
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.21687
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22577
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2203
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2091.52400
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88923734
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.12231571
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7914.51370
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 88 -
Rwork0.202 1757 -
obs--69.2 %
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)
13.8156-0.04030.56382.06391.00255.15220.1718-0.1067-0.27110.10530.06040.00370.66750.234-0.2322-0.04830.02570.0101-0.0214-0.0246-0.01245.4212.36159.914
23.21750.29420.01232.4328-1.18662.9587-0.06650.32590.14960.1014-0.0914-0.1061-0.35630.1940.1579-0.0546-0.02040.03030.05620.0355-0.0535-9.2140.43455.036
32.26630.14140.23392.4233-0.24142.59520.0156-0.09360.05050.2756-0.0242-0.0147-0.1015-0.06280.0086-0.02130.0240.06240.0575-0.0421-0.006220.62930.2583.346
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A410 - 575
2X-RAY DIFFRACTION2B408 - 575
3X-RAY DIFFRACTION3C411 - 574

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