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- PDB-5h1y: Crystal structure of the DDX41 DEAD domain in complex with SO42- ... -

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Basic information

Entry
Database: PDB / ID: 5h1y
TitleCrystal structure of the DDX41 DEAD domain in complex with SO42- and Mg2+
ComponentsProbable ATP-dependent RNA helicase DDX41
KeywordsHYDROLASE / DNA sensor CDNs receptor ATPase
Function / homology
Function and homology information


STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / cGAS/STING signaling pathway / Regulation of innate immune responses to cytosolic DNA / cellular response to interferon-beta / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / defense response to virus ...STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / cGAS/STING signaling pathway / Regulation of innate immune responses to cytosolic DNA / cellular response to interferon-beta / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / defense response to virus / cell differentiation / cell population proliferation / RNA helicase activity / RNA helicase / mRNA binding / apoptotic process / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / membrane / cytosol
Similarity search - Function
DDX41, DEAD-box helicase domain / 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 ...DDX41, DEAD-box helicase domain / 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
Probable ATP-dependent RNA helicase DDX41
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsJiang, Y. / Ouyang, S. / Liu, Z.J.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Protein Cell / Year: 2017
Title: Structural and functional analyses of human DDX41 DEAD domain
Authors: Jiang, Y. / Zhu, Y. / Qiu, W. / Liu, Y.J. / Cheng, G. / Liu, Z.J. / Ouyang, S.
History
DepositionOct 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX41
B: Probable ATP-dependent RNA helicase DDX41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6796
Polymers63,4392
Non-polymers2414
Water2,846158
1
A: Probable ATP-dependent RNA helicase DDX41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8403
Polymers31,7191
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ATP-dependent RNA helicase DDX41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8403
Polymers31,7191
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.881, 62.746, 92.881
Angle α, β, γ (deg.)90.00, 94.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable ATP-dependent RNA helicase DDX41 / DEAD box protein 41 / DEAD box protein abstrakt homolog


Mass: 31719.318 Da / Num. of mol.: 2 / Fragment: UNP residues 153-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX41, ABS
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9UJV9, RNA helicase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.19 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium sulfate, 25% PEG 3,350, 0.1M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 23367 / % possible obs: 98.6 % / Redundancy: 3.4 % / Rsym value: 0.547 / Net I/σ(I): 21.4
Reflection shellResolution: 2.26→2.33 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.34 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data processing
PHENIXmodel building
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FE2

3fe2


Resolution: 2.26→35.891 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.52
RfactorNum. reflection% reflection
Rfree0.2328 1201 5.14 %
Rwork0.1857 --
obs0.1883 23367 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.26→35.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 0 158 4028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093942
X-RAY DIFFRACTIONf_angle_d1.2345294
X-RAY DIFFRACTIONf_dihedral_angle_d14.4721550
X-RAY DIFFRACTIONf_chiral_restr0.079591
X-RAY DIFFRACTIONf_plane_restr0.005669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2584-2.34880.32461240.2582324X-RAY DIFFRACTION93
2.3488-2.45570.33061360.24522424X-RAY DIFFRACTION97
2.4557-2.58510.31311300.21942410X-RAY DIFFRACTION97
2.5851-2.74710.31661240.21892469X-RAY DIFFRACTION98
2.7471-2.95910.28251220.20822462X-RAY DIFFRACTION99
2.9591-3.25670.25861380.2032481X-RAY DIFFRACTION100
3.2567-3.72750.22311290.16992550X-RAY DIFFRACTION100
3.7275-4.69460.20061390.14942504X-RAY DIFFRACTION100
4.6946-35.89560.16471590.16312542X-RAY DIFFRACTION99

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