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- PDB-6m6q: Crystal structure of Caenorhabditis elegans Dicer-related helicas... -

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Basic information

Entry
Database: PDB / ID: 6m6q
TitleCrystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) N-terminal domain
ComponentsDicer Related Helicase
KeywordsSIGNALING PROTEIN / RNA Interference (RNAi) / RNA Helicase / CARD
Function / homology
Function and homology information


Negative regulators of DDX58/IFIH1 signaling / ISG15 antiviral mechanism / metaphase plate / Ub-specific processing proteases / P granule assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / ATP-dependent activity, acting on RNA / P granule / RNA polymerase binding ...Negative regulators of DDX58/IFIH1 signaling / ISG15 antiviral mechanism / metaphase plate / Ub-specific processing proteases / P granule assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / ATP-dependent activity, acting on RNA / P granule / RNA polymerase binding / antiviral innate immune response / helicase activity / condensed nuclear chromosome / double-stranded RNA binding / single-stranded RNA binding / ATP hydrolysis activity / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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. ...RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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
Helicase ATP-binding domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsLi, K. / Zheng, J. / Wirawan, M. / Xiong, Z. / Fedorova, O. / Griffin, P. / Plyle, A. / Luo, D.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Insights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3).
Authors: Li, K. / Zheng, J. / Wirawan, M. / Trinh, N.M. / Fedorova, O. / Griffin, P.R. / Pyle, A.M. / Luo, D.
History
DepositionMar 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dicer Related Helicase
B: Dicer Related Helicase


Theoretical massNumber of molelcules
Total (without water)79,4242
Polymers79,4242
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-6 kcal/mol
Surface area33140 Å2
Unit cell
Length a, b, c (Å)93.180, 93.180, 215.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 4 - 328 / Label seq-ID: 4 - 328

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Dicer Related Helicase


Mass: 39712.227 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: drh-3, CELE_D2005.5, D2005.5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93413
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.2 M ammonium fluoride (pH 6.2), 20% w/v polyethylene glycol 3350, 5 mM dithiothreitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9998 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.8→85.56 Å / Num. obs: 24012 / % possible obs: 99.3 % / Redundancy: 11.1 % / Biso Wilson estimate: 66.9 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.146 / Χ2: 1.19 / Net I/σ(I): 10.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3401 / CC1/2: 0.752 / Rrim(I) all: 0.992 / Χ2: 0.83 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
iMOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→70.64 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.856 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R: 1.539 / ESU R Free: 0.401 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28597 1201 5 %RANDOM
Rwork0.23374 ---
obs0.23632 22582 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 80.548 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.64 Å2
Refinement stepCycle: 1 / Resolution: 2.8→70.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5218 0 0 138 5356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135387
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174977
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.6537270
X-RAY DIFFRACTIONr_angle_other_deg1.1391.58511569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2625630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48822.205331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.87515997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8381541
X-RAY DIFFRACTIONr_chiral_restr0.0530.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025964
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021211
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.4748.3522496
X-RAY DIFFRACTIONr_mcbond_other6.4738.352495
X-RAY DIFFRACTIONr_mcangle_it9.65112.5133116
X-RAY DIFFRACTIONr_mcangle_other9.6512.5163117
X-RAY DIFFRACTIONr_scbond_it5.8958.8522891
X-RAY DIFFRACTIONr_scbond_other5.8958.8522891
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.17413.0624149
X-RAY DIFFRACTIONr_long_range_B_other14.49521564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9157 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 81 -
Rwork0.336 1636 -
obs--98.4 %

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