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- PDB-6l5m: Crystal structure of human DEAD-box RNA helicase DDX21 in complex... -

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Basic information

Entry
Database: PDB / ID: 6l5m
TitleCrystal structure of human DEAD-box RNA helicase DDX21 in complex with AMP
ComponentsNucleolar RNA helicase 2
KeywordsRNA BINDING PROTEIN / with AMP
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 MONOPHOSPHATE / Nucleolar RNA helicase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 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 / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
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
B: Nucleolar RNA helicase 2
C: Nucleolar RNA helicase 2
D: Nucleolar RNA helicase 2
E: Nucleolar RNA helicase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,15410
Polymers211,4175
Non-polymers1,7365
Water1,04558
1
A: Nucleolar RNA helicase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6312
Polymers42,2831
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-4 kcal/mol
Surface area18570 Å2
MethodPISA
2
B: Nucleolar RNA helicase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6312
Polymers42,2831
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-2 kcal/mol
Surface area18430 Å2
MethodPISA
3
C: Nucleolar RNA helicase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6312
Polymers42,2831
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-3 kcal/mol
Surface area18700 Å2
MethodPISA
4
D: Nucleolar RNA helicase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6312
Polymers42,2831
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-2 kcal/mol
Surface area18600 Å2
MethodPISA
5
E: Nucleolar RNA helicase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6312
Polymers42,2831
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-2 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.390, 219.070, 126.390
Angle α, β, γ (deg.)90.000, 90.790, 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: 42283.492 Da / Num. of mol.: 5
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-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 19% pEG3350, 0.18M ammonium citrate, 40mM myo-inositol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.7→126.378 Å / Num. obs: 51933 / % possible obs: 95.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 30.36 Å2 / Rsym value: 0.209 / Net I/σ(I): 6.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 51933 / Rsym value: 0.682 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→36.51 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.846 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.356
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2580 4.97 %RANDOM
Rwork0.207 ---
obs0.21 51895 95.9 %-
Displacement parametersBiso max: 113.48 Å2 / Biso mean: 25.7 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-5.3851 Å20 Å2-10.8173 Å2
2---3.316 Å20 Å2
3----2.0691 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.7→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14470 0 115 58 14643
Biso mean--21.85 8.89 -
Num. residues----1830
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5340SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2580HARMONIC5
X-RAY DIFFRACTIONt_it14870HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1945SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15858SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14870HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg20060HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion20.79
LS refinement shellResolution: 2.7→2.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3065 49 4.72 %
Rwork0.2575 989 -
all0.2605 1038 -
obs--99.62 %

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