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- PDB-9t99: Structure of C. elegans Dicer-related helicase 1 (DRH1) bound to ... -

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Basic information

Entry
Database: PDB / ID: 9t99
TitleStructure of C. elegans Dicer-related helicase 1 (DRH1) bound to blunt end 5'P-dsRNA
Components
  • Dicer-related helicase
  • RNA (5'-R(P*GP*GP*UP*AP*GP*CP*GP*CP*UP*AP*CP*C)-3')
  • RNA (5'-R(P*GP*GP*UP*AP*GP*UP*CP*UP*AP*CP*C)-3')
KeywordsRNA BINDING PROTEIN / RIG-I like RNA helicase / Zn-containing C-terminal domain (CTD)
Function / homology
Function and homology information


Ub-specific processing proteases / regulatory ncRNA-mediated post-transcriptional gene silencing / helicase activity / nucleic acid binding / innate immune response / 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 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
ADENOSINE-5'-DIPHOSPHATE / RNA / RNA (> 10) / Dicer-related helicase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsCusack, S. / Uchikawa, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: To Be Published
Title: Structure of C. elegans Dicer-related helicase 1 (DRH1) bound to blunt end 5'P-dsRNA
Authors: Cusack, S. / Uchikawa, E.
History
DepositionNov 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dicer-related helicase
S: RNA (5'-R(P*GP*GP*UP*AP*GP*UP*CP*UP*AP*CP*C)-3')
X: RNA (5'-R(P*GP*GP*UP*AP*GP*CP*GP*CP*UP*AP*CP*C)-3')
Y: RNA (5'-R(P*GP*GP*UP*AP*GP*CP*GP*CP*UP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6376
Polymers94,1444
Non-polymers4932
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-45 kcal/mol
Surface area38130 Å2
Unit cell
Length a, b, c (Å)134.354, 134.354, 221.301
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Components on special symmetry positions
IDModelComponents
11A-1261-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dicer-related helicase / RNA helicase


Mass: 83006.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DRH1 residues 291-1017 with E431Q mutation. N-terminal G retained after Tobacco Etch Virus protease cleavage of His-tag.
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: drh-1, CELE_F15B10.2, F15B10.2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: G5EDI8

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RNA chain , 2 types, 3 molecules SXY

#2: RNA chain RNA (5'-R(P*GP*GP*UP*AP*GP*UP*CP*UP*AP*CP*C)-3')


Mass: 3483.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*GP*GP*UP*AP*GP*CP*GP*CP*UP*AP*CP*C)-3')


Mass: 3827.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 82 molecules

#4: 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
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Directly after size exclusion chromatography DRH-1deltaN_E431Q was concentrated 10 mg/ml and mixed with 12 dsRNAp in a 1:2 molar ratio, ADP-AlF4 (adenosine-5-diphosphate with aluminium ...Details: Directly after size exclusion chromatography DRH-1deltaN_E431Q was concentrated 10 mg/ml and mixed with 12 dsRNAp in a 1:2 molar ratio, ADP-AlF4 (adenosine-5-diphosphate with aluminium fluoride) and 2 mM MgCl2 were added then incubated for 30 minutes on ice. The complex was mixed with reservoir buffer (0.2 M tri Ammonium citrate 20 % PEG3350 or 0.2 M Sodium malonate dibasic monohydrate 20% PEG3350) in 1:1 ratio. Crystals grew in two weeks at 4 C.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.18→114.846 Å / Num. obs: 44595 / % possible obs: 84.2 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.037 / Rrim(I) all: 0.087 / Net I/σ(I): 11
Reflection shellResolution: 2.18→2.335 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.549 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2232 / CC1/2: 0.514 / % possible all: 23

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→72.08 Å / SU ML: 0.304 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.0184
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2569 2277 5.11 %
Rwork0.2179 42311 -
obs0.2199 44588 84.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.19 Å2
Refinement stepCycle: LAST / Resolution: 2.18→72.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 748 28 80 6440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00276560
X-RAY DIFFRACTIONf_angle_d0.50019036
X-RAY DIFFRACTIONf_chiral_restr0.03871059
X-RAY DIFFRACTIONf_plane_restr0.00441036
X-RAY DIFFRACTIONf_dihedral_angle_d14.91772722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.230.4760.335451X-RAY DIFFRACTION1.76
2.23-2.280.3689220.3464473X-RAY DIFFRACTION15.17
2.28-2.340.3466860.3111641X-RAY DIFFRACTION53.47
2.34-2.40.29951510.28752765X-RAY DIFFRACTION88.98
2.4-2.470.32761830.27883031X-RAY DIFFRACTION98.26
2.47-2.550.28981820.28153051X-RAY DIFFRACTION99.6
2.55-2.640.37771570.33713109X-RAY DIFFRACTION99.27
2.64-2.750.35571690.31393095X-RAY DIFFRACTION99.45
2.75-2.870.34271620.27273101X-RAY DIFFRACTION99.33
2.87-3.020.27821760.25033100X-RAY DIFFRACTION99.24
3.02-3.210.27661600.25753105X-RAY DIFFRACTION99.18
3.21-3.460.28381470.24633140X-RAY DIFFRACTION98.89
3.46-3.810.2441780.20373104X-RAY DIFFRACTION98.74
3.81-4.360.2261790.19053111X-RAY DIFFRACTION98.44
4.36-5.490.22231570.16743155X-RAY DIFFRACTION98.02
5.49-72.080.22531620.18943279X-RAY DIFFRACTION96.85
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)
10.6302256162850.0706696980247-0.00600798742261.58018772882-0.9031619768481.52206349723-0.0507880614011-0.08681346759160.0132216788461-0.2701525176080.04641322884110.2500808764830.207957897896-0.0112124815479-0.0001415740759720.3204653186870.00611523112467-0.03871523147770.378731728676-0.02558894507010.402608730307-11.5036003295-22.4119851764-43.6793443289
20.8415796890120.61053247029-1.190853823561.21866570876-1.077750842451.975296331-0.226856631838-0.028485220639-0.215046199691-0.2905421041080.0115168151274-0.3129077354550.5491085324130.4063780618140.002344930923010.762880093464-0.0193134261050.05393851537940.6716212281110.09869033856550.5894228755021.43671324609-47.5515913985-27.4363597718
30.9008573338890.2841707530850.2895628368731.57238624858-0.265970469220.6400959473960.0360063207375-0.026722613438-0.0638765870746-0.0171254587099-0.0728017618992-0.2059022014710.09347781940220.156999339516-2.55038825427E-50.2991759687060.05357859663890.01355167444160.420647665540.05105607849760.3373775357067.28044389484-21.9087241592-35.2650431775
40.004103131859090.04099599942350.05540231929340.1521703797770.1445545339420.115732872564-0.415050227094-0.0875538623803-0.7587617486540.354848862014-0.09931685899630.008344399555820.1654282601-0.2372699199580.0001110081606081.589495397520.05807987356210.02492948523191.5604073793-0.1606004878990.883976533729-14.6505585808-14.13538942460.905242763378
50.2855382735550.0162921009395-0.01743500377970.574108295446-0.1984711187380.03007693067990.289953568278-0.1881750380880.2936818641110.459367681291-0.04976540736230.194312708197-0.180860432855-0.00225702428133-6.32377657218E-50.551509501563-0.008965051846080.03043805906230.6085524523130.01872283023040.3895619168130.327758678321-27.6272364258-26.9882887334
6-0.03733841363230.00821460077224-0.01020717760590.221361832174-0.3062813827850.2147628702690.239949503490.07601016636740.05163726684690.219166900892-0.04817971431520.139680246183-0.440852970989-0.002085404272051.04838138061E-50.6462936314350.01256725201940.04799856638330.5340879724130.02270127672830.3753727130080.603732960165-28.2277505949-29.2411513303
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 290 through 556 )AA290 - 5561 - 267
22chain 'A' and (resid 557 through 796 )AA557 - 796268 - 485
33chain 'A' and (resid 797 through 1014 )AA797 - 1014486 - 700
44chain 'S' and (resid 1 through 11 )SC1 - 11
55chain 'X' and (resid 1 through 12 )XD1 - 12
66chain 'Y' and (resid 13 through 24 )YE13 - 24

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