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- PDB-6l5o: Crystal structure of human DEAD-box RNA helicase DDX21 at post-hy... -

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Basic information

Entry
Database: PDB / ID: 6l5o
TitleCrystal structure of human DEAD-box RNA helicase DDX21 at post-hydrolysis state
ComponentsNucleolar RNA helicase 2
KeywordsRNA BINDING PROTEIN / ADP bound complex
Function / homology
Function and homology information


RNA polymerase inhibitor activity / 7SK snRNA binding / R-loop processing / central nervous system projection neuron axonogenesis / positive regulation of myeloid dendritic cell cytokine production / B-WICH complex / miRNA binding / positive regulation of transcription by RNA polymerase III / negative regulation of transcription by RNA polymerase I / snoRNA binding ...RNA polymerase inhibitor activity / 7SK snRNA binding / R-loop processing / central nervous system projection neuron axonogenesis / positive regulation of myeloid dendritic cell cytokine production / B-WICH complex / miRNA binding / positive regulation of transcription by RNA polymerase III / negative regulation of transcription by RNA polymerase I / snoRNA binding / positive regulation of transcription by RNA polymerase I / response to exogenous dsRNA / Major pathway of rRNA processing in the nucleolus and cytosol / neuron projection maintenance / B-WICH complex positively regulates rRNA expression / microtubule cytoskeleton organization / osteoblast differentiation / rRNA processing / double-stranded RNA binding / chromosome / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / transcription by RNA polymerase II / RNA helicase activity / rRNA binding / RNA helicase / chromatin remodeling / innate immune response / mRNA binding / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
GUCT / GUCT (NUC152) domain / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / 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. ...GUCT / GUCT (NUC152) domain / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / 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
ADENOSINE-5'-DIPHOSPHATE / Nucleolar RNA helicase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChen, Z.J. / Hu, X.J. / Zhou, Z. / Li, J.X.
CitationJournal: Adv Sci / Year: 2020
Title: Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation.
Authors: Chen, Z. / Li, Z. / Hu, X. / Xie, F. / Kuang, S. / Zhan, B. / Gao, W. / Chen, X. / Gao, S. / Li, Y. / Wang, Y. / Qian, F. / Ding, C. / Gan, J. / Ji, C. / Xu, X. / Zhou, Z. / Huang, J. / He, H.H. / Li, J.
History
DepositionOct 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Data collection / Category: citation_editor
Revision 1.2Aug 12, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleolar RNA helicase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2824
Polymers41,7391
Non-polymers5443
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-17 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.460, 43.830, 72.440
Angle α, β, γ (deg.)90.000, 115.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nucleolar RNA helicase 2 / DEAD box protein 21 / Gu-alpha / Nucleolar RNA helicase Gu / Nucleolar RNA helicase II / RH II/Gu


Mass: 41738.848 Da / Num. of mol.: 1 / Mutation: G401, K402, K403, T404, Q405 deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR30, RNA helicase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% pEG3350, 0.2m Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.8→65.307 Å / Num. obs: 33164 / % possible obs: 94.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 15.31 Å2 / Rpim(I) all: 0.065 / Rrim(I) all: 0.145 / Rsym value: 0.129 / Net I/av σ(I): 4.9 / Net I/σ(I): 7.9 / Num. measured all: 139159
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.940.67311964449040.3540.7650.6732.396.1
1.9-2.014.20.4461.51968546600.2260.5040.4463.396.8
2.01-2.1540.3082.21709142790.1610.350.3084.594.7
2.15-2.324.10.2133.21639039930.1090.2410.2136.194.9
2.32-2.554.40.1584.41631337360.0790.1780.1588.196.1
2.55-2.854.10.1235.61325332560.0630.1390.1239.692.5
2.85-3.294.50.0867.91340929690.0420.0960.08612.794.9
3.29-4.024.30.0649.61048324280.0320.0720.06416.291.7
4.02-5.694.40.05910.3843819020.0290.0660.05918.291.8
5.69-36.9064.30.04611445310370.0230.0520.04618.189

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→36.906 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.87
RfactorNum. reflection% reflection
Rfree0.2096 1713 5.17 %
Rwork0.1755 --
obs0.1773 33149 94.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.64 Å2 / Biso mean: 20.8026 Å2 / Biso min: 3.99 Å2
Refinement stepCycle: final / Resolution: 1.8→36.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 34 148 3119
Biso mean--17.82 25.32 -
Num. residues----372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073064
X-RAY DIFFRACTIONf_angle_d0.8654143
X-RAY DIFFRACTIONf_chiral_restr0.058460
X-RAY DIFFRACTIONf_plane_restr0.005533
X-RAY DIFFRACTIONf_dihedral_angle_d9.1022569
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.8530.28141360.2313259394
1.853-1.91280.26051360.2073272097
1.9128-1.98110.22431220.2108268697
1.9811-2.06050.21381470.1851263996
2.0605-2.15420.21821420.1728259393
2.1542-2.26780.21471370.1751258794
2.2678-2.40980.20911530.1715268196
2.4098-2.59590.21071300.1726263795
2.5959-2.8570.231620.1783252291
2.857-3.27020.2131350.1718264995
3.2702-4.11920.17511590.1553253791
4.1192-36.90.19721540.1677259290

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