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- PDB-6m6r: Crystal structure of Caenorhabditis elegans Dicer-related helicas... -

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Basic information

Entry
Database: PDB / ID: 6m6r
TitleCrystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) C-terminal domain with 5'-ppp 8-mer ssRNA
Components
  • Dicer Related Helicase
  • RNA (5'-R(*(GTP)P*GP*CP*CP*GP*CP*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


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 / ATP-dependent activity, acting on RNA / siRNA processing / 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 / ATP-dependent activity, acting on RNA / siRNA processing / 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
RNA / Helicase ATP-binding domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 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 / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNA (5'-R(*(GTP)P*GP*CP*CP*GP*CP*CP*C)-3')
A: Dicer Related Helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0873
Polymers23,0222
Non-polymers651
Water2,234124
1
B: RNA (5'-R(*(GTP)P*GP*CP*CP*GP*CP*CP*C)-3')
A: Dicer Related Helicase
hetero molecules

B: RNA (5'-R(*(GTP)P*GP*CP*CP*GP*CP*CP*C)-3')
A: Dicer Related Helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1756
Polymers46,0444
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4770 Å2
ΔGint-10 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.843, 56.843, 131.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1326-

HOH

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Components

#1: RNA chain RNA (5'-R(*(GTP)P*GP*CP*CP*GP*CP*CP*C)-3')


Mass: 2676.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Dicer Related Helicase


Mass: 20345.457 Da / Num. of mol.: 1 / 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 25% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2819 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: 1.2819 Å / Relative weight: 1
ReflectionResolution: 1.89→43.04 Å / Num. obs: 17289 / % possible obs: 96.3 % / Redundancy: 9.2 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.158 / Net I/σ(I): 12
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.715 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 984 / CC1/2: 0.378 / Rrim(I) all: 1.95 / % possible all: 88.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.89→43.036 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.98
RfactorNum. reflection% reflection
Rfree0.2213 825 4.78 %
Rwork0.1777 --
obs0.1797 17265 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→43.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 178 1 124 1669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081598
X-RAY DIFFRACTIONf_angle_d0.9912185
X-RAY DIFFRACTIONf_dihedral_angle_d9.8311307
X-RAY DIFFRACTIONf_chiral_restr0.058243
X-RAY DIFFRACTIONf_plane_restr0.005244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-2.00810.26211270.24442555X-RAY DIFFRACTION92
2.0081-2.16320.2191320.19762658X-RAY DIFFRACTION95
2.1632-2.38080.26891310.17842701X-RAY DIFFRACTION96
2.3808-2.72530.22191460.18182730X-RAY DIFFRACTION96
2.7253-3.43340.21391460.17892790X-RAY DIFFRACTION97
3.4334-43.030.20711430.16223006X-RAY DIFFRACTION98
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)
10.581-0.1444-0.73150.37450.16861.039-0.662-0.12520.77340.4294-0.23470.0437-0.45730.1041-0.19110.5990.1697-0.25470.4283-0.06630.65527.346829.38393.5067
20.2404-0.14170.11360.0721-0.0720.1213-0.092-0.31010.27520.50780.0803-0.0867-0.0281-0.06610.00330.221-0.0002-0.02890.2461-0.0560.246228.69720.797226.8874
30.8697-0.1125-0.28680.2617-0.05490.43390.0995-0.0505-0.08210.0542-0.03080.01730.0415-0.084100.15410.0111-0.03620.18560.02110.152123.03077.806912.1807
40.1418-0.0925-0.20071.74410.0920.23260.3435-0.41060.2156-0.2452-0.37840.029-0.04470.4883-0.03690.239-0.06650.03950.44190.0030.173329.18159.7378-7.8729
50.30910.2436-0.45690.41690.14791.21830.10640.2427-0.06810.07470.05490.01120.0846-0.0560.00050.16080.0112-0.02340.25570.00220.19624.03047.25573.202
61.62450.0260.74690.46520.48291.98990.0606-0.06070.07440.08740.0295-0.01810.1129-0.05240.03860.09760.00250.00870.15060.03820.161126.346212.359116.2076
72.563-0.01750.2712.11220.94262.43760.12560.4323-0.3117-0.12-0.0558-0.36610.50850.35590.61970.22920.0466-0.02160.3594-0.06350.222929.97411.5368-8.3506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 8 )
2X-RAY DIFFRACTION2chain 'A' and (resid 940 through 948 )
3X-RAY DIFFRACTION3chain 'A' and (resid 949 through 986 )
4X-RAY DIFFRACTION4chain 'A' and (resid 987 through 998 )
5X-RAY DIFFRACTION5chain 'A' and (resid 999 through 1029 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1030 through 1077 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1078 through 1105 )

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