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- PDB-7liu: DDX3X bound to ATP analog and remodeled RNA:DNA hybrid -

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Basic information

Entry
Database: PDB / ID: 7liu
TitleDDX3X bound to ATP analog and remodeled RNA:DNA hybrid
Components
  • 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
  • ATP-dependent RNA helicase DDX3X
KeywordsRNA-BINDING PROTEIN/DNA / RNA / DEAD-box helicase / RNA helicase / ATPase / RNA BINDING PROTEIN / RNA-BINDING PROTEIN-DNA / RNA complex
Function / homology
Function and homology information


positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / CTPase activity / positive regulation of translation in response to endoplasmic reticulum stress / gamete generation / positive regulation of chemokine (C-C motif) ligand 5 production / eukaryotic initiation factor 4E binding / RNA strand annealing activity / protein localization to cytoplasmic stress granule / positive regulation of mitochondrial translation ...positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / CTPase activity / positive regulation of translation in response to endoplasmic reticulum stress / gamete generation / positive regulation of chemokine (C-C motif) ligand 5 production / eukaryotic initiation factor 4E binding / RNA strand annealing activity / protein localization to cytoplasmic stress granule / positive regulation of mitochondrial translation / positive regulation of protein K63-linked ubiquitination / cellular response to arsenic-containing substance / NLRP3 inflammasome complex / poly(A) binding / gamma-tubulin binding / P granule / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to osmotic stress / transcription factor binding / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of intrinsic apoptotic signaling pathway / ribosomal small subunit binding / lipid homeostasis / cytoplasmic pattern recognition receptor signaling pathway / cell leading edge / positive regulation of interferon-alpha production / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of translational initiation / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / Dengue virus activates/modulates innate and adaptive immune responses / positive regulation of G1/S transition of mitotic cell cycle / intrinsic apoptotic signaling pathway / positive regulation of type I interferon production / signaling adaptor activity / positive regulation of interferon-beta production / translation initiation factor binding / protein serine/threonine kinase activator activity / DNA helicase activity / stress granule assembly / cytosolic ribosome assembly / positive regulation of translation / cellular response to virus / chromosome segregation / translational initiation / Wnt signaling pathway / negative regulation of cell growth / positive regulation of non-canonical NF-kappaB signal transduction / response to virus / RNA stem-loop binding / mRNA 5'-UTR binding / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / ribonucleoside triphosphate phosphatase activity / positive regulation of cell growth / lamellipodium / secretory granule lumen / ficolin-1-rich granule lumen / cell differentiation / RNA helicase activity / negative regulation of translation / intracellular signal transduction / positive regulation of apoptotic process / RNA helicase / cadherin binding / negative regulation of gene expression / innate immune response / mRNA binding / centrosome / positive regulation of gene expression / GTPase activity / negative regulation of apoptotic process / Neutrophil degranulation / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / DNA-templated transcription / 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
Chem-08T / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / ATP-dependent RNA helicase DDX3X
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.001 Å
AuthorsEnemark, E.J. / Yu, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institute of General Medical Sciences (NIGMS)NIGMS 1 R35 GM 136313-01 United States
CitationJournal: To Be Published
Title: DDX3X bound to ATP analog and remodeled RNA:DNA hybrid
Authors: Enemark, E.J. / Yu, S.
History
DepositionJan 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.0Aug 12, 2026Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _chem_comp.formula / _pdbx_entry_details.has_protein_modification
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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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
X: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
Y: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4608
Polymers110,4274
Non-polymers1,0334
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-51 kcal/mol
Surface area40310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.476, 114.476, 281.793
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11chain A
21chain B
12chain X
22chain Y

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPTYRTYRchain AAA135 - 5763 - 444
21ASPASPTYRTYRchain BBB135 - 5763 - 444
12GGDCDCchain XXC701 - 7141 - 14
22GGDCDCchain YYD701 - 7141 - 14

NCS ensembles :
ID
1
2

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Components

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


Mass: 50817.770 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: DNA/RNA hybrid 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'


Mass: 4395.755 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Sequence design is as published in Mallam et al, Nature 2012 (PDB 4DB4)
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-08T / [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium


Mass: 492.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14BeF3N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.91 Å3/Da / Density % sol: 74.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPEs pH 7.5, 16% PEG 3350, 0.1 M Li3Citrate, 0.1 M Na3Citrate, 2% benzamidine-HCl, 5 mM ADP-BeF3

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 9, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 43593 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 85.2 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.121 / Rsym value: 0.113 / Net I/σ(I): 20.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4265 / CC1/2: 0.641 / Rpim(I) all: 0.379 / Rrim(I) all: 0.964 / Rsym value: 0.882 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PXA

4pxa


Resolution: 3.001→40.54 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2412 2197 5.04 %
Rwork0.2096 41375 -
obs0.2112 43572 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.97 Å2 / Biso mean: 89.6588 Å2 / Biso min: 35.46 Å2
Refinement stepCycle: final / Resolution: 3.001→40.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7006 582 64 8 7660
Biso mean--85.54 60.21 -
Num. residues----912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087870
X-RAY DIFFRACTIONf_angle_d1.08310788
X-RAY DIFFRACTIONf_chiral_restr0.0541192
X-RAY DIFFRACTIONf_plane_restr0.0071300
X-RAY DIFFRACTIONf_dihedral_angle_d5.9834692
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4408X-RAY DIFFRACTION2.67TORSIONAL
12B4408X-RAY DIFFRACTION2.67TORSIONAL
21X300X-RAY DIFFRACTION2.67TORSIONAL
22Y300X-RAY DIFFRACTION2.67TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.001-3.06570.36761330.3252248098
3.0657-3.1370.33071470.30672520100
3.137-3.21550.36391410.29272548100
3.2155-3.30240.31581090.29422585100
3.3024-3.39950.27861140.26722561100
3.3995-3.50910.30341470.2492544100
3.5091-3.63450.33911190.25242588100
3.6345-3.77990.29861250.24652582100
3.7799-3.95180.26451340.24342598100
3.9518-4.160.27561400.22712562100
4.16-4.42030.25361450.19882589100
4.4203-4.76110.25521490.18732577100
4.7611-5.23930.20881690.19132575100
5.2393-5.99540.21441530.2062607100
5.9954-7.54560.20611280.18952665100
7.5456-40.540.15781440.14482794100

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