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- PDB-6m6s: Crystal structure of Caenorhabditis elegans Dicer-related helicas... -

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Basic information

Entry
Database: PDB / ID: 6m6s
TitleCrystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) C-terminal domain with 5'-ppp 12-mer dsRNA
Components
  • Dicer Related Helicase
  • RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / RNA Interference (RNAi) / RNA Helicase / HYDROLASE / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


Modulation of host responses by IFN-stimulated genes / ISG15 antiviral mechanism / metaphase plate / Negative regulators of DDX58/IFIH1 signaling / Ub-specific processing proteases / P granule assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / ATP-dependent activity, acting on RNA / P granule ...Modulation of host responses by IFN-stimulated genes / ISG15 antiviral mechanism / metaphase plate / Negative regulators of DDX58/IFIH1 signaling / 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 / condensed nuclear chromosome / helicase activity / double-stranded RNA binding / single-stranded RNA binding / innate immune response / ATP hydrolysis activity / ATP binding / metal ion 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 domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal 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 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / Helicase ATP-binding domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
D: RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8566
Polymers48,7264
Non-polymers1312
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-16 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.775, 93.090, 133.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Dicer Related Helicase


Mass: 20345.457 Da / Num. of mol.: 2 / Fragment: C-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: RNA chain RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')


Mass: 4017.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris pH 7.5, 30% w/v polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→43.96 Å / Num. obs: 56358 / % possible obs: 99.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.064 / Χ2: 0.88 / Net I/σ(I): 14.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.761 / Num. unique obs: 2845 / CC1/2: 0.586 / Rrim(I) all: 1.021 / Χ2: 0.75 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_1137refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M6R

6m6r


Resolution: 1.6→23.03 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 19.74
RfactorNum. reflection% reflection
Rfree0.1988 2858 5.08 %
Rwork0.1692 --
obs0.1707 56281 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 534 2 332 3529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173452
X-RAY DIFFRACTIONf_angle_d1.8814775
X-RAY DIFFRACTIONf_dihedral_angle_d20.0011399
X-RAY DIFFRACTIONf_chiral_restr0.125532
X-RAY DIFFRACTIONf_plane_restr0.009499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62760.2941360.26072639X-RAY DIFFRACTION100
1.6276-1.65720.27441390.24032636X-RAY DIFFRACTION100
1.6572-1.6890.27391450.22662678X-RAY DIFFRACTION100
1.689-1.72350.25261340.21952632X-RAY DIFFRACTION100
1.7235-1.7610.26031470.20372663X-RAY DIFFRACTION100
1.761-1.80190.22731450.19992640X-RAY DIFFRACTION100
1.8019-1.8470.21961570.18792631X-RAY DIFFRACTION100
1.847-1.89690.22331300.18252698X-RAY DIFFRACTION100
1.8969-1.95270.22321330.17962655X-RAY DIFFRACTION100
1.9527-2.01570.19961410.17412691X-RAY DIFFRACTION100
2.0157-2.08760.21121540.17272658X-RAY DIFFRACTION100
2.0876-2.17120.20461440.16672655X-RAY DIFFRACTION100
2.1712-2.26990.19951520.16382701X-RAY DIFFRACTION100
2.2699-2.38950.19751580.16712660X-RAY DIFFRACTION100
2.3895-2.5390.19171310.16592678X-RAY DIFFRACTION99
2.539-2.73470.21251330.17742704X-RAY DIFFRACTION99
2.7347-3.00940.21871470.1782714X-RAY DIFFRACTION99
3.0094-3.44360.15971330.15492708X-RAY DIFFRACTION98
3.4436-4.33390.16521460.13892683X-RAY DIFFRACTION97
4.3339-23.030.18481530.15882699X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.79570.5947-0.05641.8271-0.38941.9842-0.04220.2065-0.0858-0.13570.0904-0.00020.0437-0.0776-0.04530.13040.0002-0.00780.0862-0.00060.072-11.9244-14.7492-1.2914
21.44050.1691-0.23692.1788-0.58312.5555-0.0254-0.0897-0.1585-0.056-0.02390.05360.12860.24160.02310.1626-0.014-0.03940.20640.06610.1212-7.6694-33.645632.6755
30.332-0.58950.42361.0338-0.76830.5337-0.0025-0.2722-0.2982-0.21070.06260.09410.90980.1667-0.08640.54580.10690.01930.29130.06310.2546-8.3833-37.35678.1379
41.5383-0.1622-0.91390.2817-1.00285.0269-0.0332-0.2563-0.2735-0.6842-0.12840.09281.12621.0041-0.07760.6305-0.0486-0.02550.38250.02440.2454-9.6433-39.031410.3231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

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