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- PDB-8swb: RNase H complex with streopure ASO and RNA -

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Basic information

Entry
Database: PDB / ID: 8swb
TitleRNase H complex with streopure ASO and RNA
Components
  • DNA (5'-R(*(OMC)P*(N7X)P*(T39)P*(C5L)P*(A2M))-D(P*(SC)P*(PST)P*(SC)P*AP*(SC)P*(SC)P*(RC)P*(AS)P*(SC)P*(PST))-R(P*(6OO)P*(RFJ)P*(6OO)P*(6OO)P*(6NW))-3')
  • RNA (5'-R(*UP*GP*GP*CP*GP*AP*GP*UP*GP*GP*GP*UP*GP*AP*GP*UP*GP*AP*GP*G)-3')
  • Ribonuclease H1
KeywordsHYDROLASE/RNA / Complex of DNA(ASO) and RNA OSS stereochemistry (PS-backbone) RNase H / HYDROLASE-RNA complex
Function / homology
Function and homology information


Strand-asynchronous mitochondrial DNA replication / DNA replication, removal of RNA primer / RNA catabolic process / ribonuclease H / RNA nuclease activity / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / mitochondrial matrix / magnesium ion binding / mitochondrion / RNA binding
Similarity search - Function
Ribonuclease H1, eukaryote / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Ribonuclease H1 N-terminal domain / : / Ribosomal protein L9/RNase H1, N-terminal / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / DNA / DNA (> 10) / RNA / RNA (> 10) / Ribonuclease H1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCho, Y.-J. / Iwamoto, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Crystal structure of RNase H/RNA/PS-ASO complex at an atomic level
Authors: Iwamoto, N. / Cho, Y.-J.
History
DepositionMay 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_symm_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease H1
B: RNA (5'-R(*UP*GP*GP*CP*GP*AP*GP*UP*GP*GP*GP*UP*GP*AP*GP*UP*GP*AP*GP*G)-3')
D: DNA (5'-R(*(OMC)P*(N7X)P*(T39)P*(C5L)P*(A2M))-D(P*(SC)P*(PST)P*(SC)P*AP*(SC)P*(SC)P*(RC)P*(AS)P*(SC)P*(PST))-R(P*(6OO)P*(RFJ)P*(6OO)P*(6OO)P*(6NW))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1056
Polymers29,8123
Non-polymers2933
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Chromatography including SEC and MS confirmed its complex formation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint12 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.545, 52.939, 106.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / RNA chain / DNA chain , 3 types, 3 molecules ABD

#1: Protein Ribonuclease H1 / RNase H1 / Ribonuclease H type II


Mass: 16575.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEH1, RNH1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60930, ribonuclease H
#2: RNA chain RNA (5'-R(*UP*GP*GP*CP*GP*AP*GP*UP*GP*GP*GP*UP*GP*AP*GP*UP*GP*AP*GP*G)-3')


Mass: 6614.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-R(*(OMC)P*(N7X)P*(T39)P*(C5L)P*(A2M))-D(P*(SC)P*(PST)P*(SC)P*AP*(SC)P*(SC)P*(RC)P*(AS)P*(SC)P*(PST))-R(P*(6OO)P*(RFJ)P*(6OO)P*(6OO)P*(6NW))-3')


Mass: 6621.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 113 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1:1 complex : precipitant (0.8 M ammonium sulfate, 0.1 M citrate, pH 4.0), cryoprotection: mother liquor + 1.75 M ammonium sulfate, 1 minute

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→47.36 Å / Num. obs: 18366 / % possible obs: 99.9 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.051 / Rrim(I) all: 0.154 / Net I/σ(I): 9
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1340 / Rpim(I) all: 0.795

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QK9

2qk9


Resolution: 2→42.62 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 915 5 %
Rwork0.1836 --
obs0.1856 18307 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 861 18 110 2153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082229
X-RAY DIFFRACTIONf_angle_d0.9863145
X-RAY DIFFRACTIONf_dihedral_angle_d21.502550
X-RAY DIFFRACTIONf_chiral_restr0.048343
X-RAY DIFFRACTIONf_plane_restr0.005275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.34341220.27952449X-RAY DIFFRACTION99
2.11-2.240.32011290.252439X-RAY DIFFRACTION100
2.24-2.410.32561330.23182438X-RAY DIFFRACTION100
2.41-2.650.27251140.22732470X-RAY DIFFRACTION100
2.65-3.040.28091440.21242453X-RAY DIFFRACTION100
3.04-3.830.19551310.16292514X-RAY DIFFRACTION100
3.83-100.16921420.14942629X-RAY DIFFRACTION100
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)
14.4862.122-2.23035.8033-2.35045.40850.198-0.64590.25690.2866-0.45480.1393-0.26850.26580.07480.13290.0697-0.01310.2752-0.07080.183211.034810.86820.7163
23.6765-0.12490.24525.0334-1.6324.06170.1801-0.4196-0.08120.0685-0.2378-0.30730.11330.61170.19980.17960.0237-0.03610.3681-0.07170.299619.645115.49120.2473
34.05420.2251-0.14023.6601-2.30411.6671-0.1456-0.13290.0298-0.3259-0.0411-0.70810.0785-0.18640.33940.29330.0370.06820.24870.01990.442123.54814.855713.052
41.30580.6826-1.11573.2311-2.16353.5811-0.1379-0.0946-0.2134-0.08870.005-0.26840.23930.09290.10580.23280.00250.04110.2043-0.00330.33611.58737.320415.063
56.38241.59832.38839.73595.78254.49370.0573-0.2937-0.99950.7388-0.0702-0.1781.3259-0.138-0.2230.3964-0.0368-0.05050.33870.02020.33895.24797.1821-0.5488
67.8478-1.96297.48758.601-3.05538.64980.19440.809-0.182-0.7533-0.2067-0.43220.03021.1741-0.1460.30720.00740.08530.2653-0.02810.270711.956913.4695-4.5554
71.33810.2932-1.83736.5009-4.84495.5923-0.0706-0.06760.1341-0.372-0.4347-0.370.74850.48830.43520.2970.0271-0.00290.2829-0.04030.430514.77483.99835.3688
85.6857-1.9674-0.68135.96890.98085.59180.05220.0026-0.2413-0.3802-0.21890.04120.5838-0.6170.20210.3683-0.09420.06380.38010.00030.42814.89043.807714.6758
94.0198-1.4103-1.64382.3633.22734.43210.04260.86441.9835-0.34920.2925-0.1796-3.43510.3104-0.02430.8565-0.0599-0.05840.546-0.0940.53863.534620.664323.2688
104.7991.5579-4.65256.6716-1.65464.79510.5185-0.24030.86460.2535-0.338-0.1234-0.77480.7344-0.0560.3783-0.0603-0.03270.5177-0.02110.372619.25417.987623.4203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 137 through 149 )
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 171 )
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 181 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 219 )
5X-RAY DIFFRACTION5chain 'A' and (resid 220 through 228 )
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 240 )
7X-RAY DIFFRACTION7chain 'A' and (resid 241 through 250 )
8X-RAY DIFFRACTION8chain 'A' and (resid 251 through 260 )
9X-RAY DIFFRACTION9chain 'A' and (resid 261 through 267 )
10X-RAY DIFFRACTION10chain 'A' and (resid 268 through 285 )

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