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- PDB-9e2c: Crystal structure of DEAD-box RNA helicase DDX3X R326H mutant -

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Basic information

Entry
Database: PDB / ID: 9e2c
TitleCrystal structure of DEAD-box RNA helicase DDX3X R326H mutant
ComponentsIsoform 2 of ATP-dependent RNA helicase DDX3X
KeywordsRNA BINDING PROTEIN / DEAD-box RNA helicase / liquid-liquid phase separation
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 / positive regulation of mitochondrial translation / gamete generation ...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 / positive regulation of mitochondrial translation / gamete generation / 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 / transcription factor binding / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of intrinsic apoptotic signaling pathway / lipid homeostasis / cell leading edge / 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 / translation initiation factor binding / signaling adaptor activity / stress granule assembly / intrinsic apoptotic signaling pathway / DNA helicase activity / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / positive regulation of translation / protein serine/threonine kinase activator activity / cytosolic ribosome assembly / chromosome segregation / translational initiation / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of cell growth / cellular response to virus / mRNA 5'-UTR binding / response to virus / RNA stem-loop binding / Wnt signaling pathway / 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 / positive regulation of apoptotic process / cadherin binding / 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 / 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 / cytoplasm / cytosol
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
AuthorsPrado, P.F.V. / Oliveira, J.F. / Nascimento, A.F.Z.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2022/12010-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)407904/2023-9 Brazil
CitationJournal: To Be Published
Title: DDX3X is a chloride-sensitive DEAD-box RNA helicase
Authors: Rosa e Silva, I. / Prado, P.F.V. / Benevenutti, F.Z. / Oliveira, R.R. / Passos, A.R. / Canateli, C. / Messias, I.G. / Trindade, D.M. / Bortot, L.O. / Sforca, M.L. / Nascimento, A.F.Z. / ...Authors: Rosa e Silva, I. / Prado, P.F.V. / Benevenutti, F.Z. / Oliveira, R.R. / Passos, A.R. / Canateli, C. / Messias, I.G. / Trindade, D.M. / Bortot, L.O. / Sforca, M.L. / Nascimento, A.F.Z. / Mercaldi, G.F. / Fonseca, M.C. / de Oliveira, P.S.L. / Carvalho, M. / Smetana, J.H.C. / Krepischi, A.C.V. / Franchini, K.G. / Oliveira, J.F.
History
DepositionOct 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of ATP-dependent RNA helicase DDX3X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1642
Polymers56,0721
Non-polymers921
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.347, 99.101, 105.351
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 56072.367 Da / Num. of mol.: 1 / Mutation: R326H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX3X, DBX, DDX3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: O00571, RNA helicase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.7 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 25% PEG3350, 0.2 M Lithium sulfate, 0.01 M Strontium(II) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 10, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 2.3→46.51 Å / Num. obs: 27821 / % possible obs: 99.83 % / Redundancy: 13 % / Biso Wilson estimate: 55.64 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.1137 / Net I/σ(I): 15.61
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.14 / Num. unique obs: 2700 / CC1/2: 0.665 / Rrim(I) all: 2.273 / % possible all: 99.22

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Processing

Software
NameVersionClassification
XDSBUILT=20210323data reduction
XDSBUILT=20210323data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.51 Å / SU ML: 0.4083 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2443 1392 5.01 %
Rwork0.2123 26417 -
obs0.214 27810 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.67 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 6 71 3454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263452
X-RAY DIFFRACTIONf_angle_d0.49164660
X-RAY DIFFRACTIONf_chiral_restr0.0421517
X-RAY DIFFRACTIONf_plane_restr0.0048610
X-RAY DIFFRACTIONf_dihedral_angle_d4.471470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.4781350.44922542X-RAY DIFFRACTION98.67
2.38-2.480.36071370.34482606X-RAY DIFFRACTION99.96
2.48-2.590.34471370.28462612X-RAY DIFFRACTION100
2.59-2.730.33191380.26932611X-RAY DIFFRACTION99.96
2.73-2.90.3091380.25462623X-RAY DIFFRACTION100
2.9-3.120.29461380.26912627X-RAY DIFFRACTION99.93
3.12-3.430.27341400.22492654X-RAY DIFFRACTION99.96
3.43-3.930.25341390.21262645X-RAY DIFFRACTION99.61
3.93-4.950.18131410.15812679X-RAY DIFFRACTION99.96
4.95-46.510.19971490.17742818X-RAY DIFFRACTION99.9
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)
13.04542133331-0.666182336697-0.06597159031213.286873790850.06945274634093.121536822674.84654511794E-50.00539463635929-0.366963842465-0.215554734432-0.002844128093510.3080129691450.492555725393-0.1450297800270.01741761742050.55877242082-0.0223446161248-0.03611899815810.3847017377250.03358116573440.383585883816-33.78135304662.47246847829.22822866998
24.557024713841.90876202053-1.518543980198.224397176940.1191512931486.116971987450.009470485337850.1597025683630.168477352361-0.290202168028-0.1556853054890.191438754267-0.1653376382770.1330534523040.1211482005640.6303916156650.0613843103098-0.07012122292530.451285162788-0.05414524021580.353098212656-8.938142858097.99051091246-17.4176393196
38.949367213480.4501878975412.289487971496.829076027473.672827751076.91664571186-0.169556092402-1.121194888421.883467746090.819836073182-0.07283204813240.0860682188571-1.09623189851-0.2574082230610.2901838584481.020772698520.06468057052270.03134363418410.847611206632-0.1684130407110.931349066159-10.219750706221.3440068595-3.71077085517
43.3794459765-0.658596935094-0.8639340032888.966949789371.040271017255.31624878746-0.298823499134-0.161833262011-0.1500270491270.2643873928280.2567303984580.03661329388570.610125634229-0.1396367316540.07094127908920.5253664423370.01515715986470.001153889530290.4385324140780.01787583000450.245358832951-10.95634554980.0917110979834-12.5378190275
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11(chain A and resid 134:406)134 - 4061 - 259
22(chain A and resid 407:471)407 - 471260 - 324
33(chain A and resid 472:485)472 - 485325 - 338
44(chain A and resid 486:577)486 - 574339 - 427

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