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- PDB-6vrd: Crystal structure of RNase H/RNA/PS-ASO complex at an atomic level -

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Basic information

Entry
Database: PDB / ID: 6vrd
TitleCrystal structure of RNase H/RNA/PS-ASO complex at an atomic level
Components
  • RNA (5'-R(*(OMC)P*(N7X)P*(T39)P*(C5L)P*(A2M))-D(P*(SC)P*(PST)P*(SC)P*(AS)P*(SC)P*(SC)P*(SC)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 / RNase H / Complex / RNA / ASO / DNA / HYDROLASE / 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 / 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 / RNA / RNA (> 10) / Ribonuclease H1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.299 Å
AuthorsCho, Y.-J. / Butler, D.
CitationJournal: To Be Published
Title: Crystal structure of RNase H/RNA/PS-ASO complex at an atomic level
Authors: Cho, Y.-J. / Butler, D.
History
DepositionFeb 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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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')
C: RNA (5'-R(*(OMC)P*(N7X)P*(T39)P*(C5L)P*(A2M))-D(P*(SC)P*(PST)P*(SC)P*(AS)P*(SC)P*(SC)P*(SC)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)46,9578
Polymers46,4713
Non-polymers4865
Water6,305350
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.760, 53.030, 106.477
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 33218.457 Da / Num. of mol.: 1 / Mutation: D210N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEH1, RNH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60930, ribonuclease H

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RNA chain , 2 types, 2 molecules BC

#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: RNA chain RNA (5'-R(*(OMC)P*(N7X)P*(T39)P*(C5L)P*(A2M))-D(P*(SC)P*(PST)P*(SC)P*(AS)P*(SC)P*(SC)P*(SC)P*(AS)P*(SC)P*(PST))-R(P*(6OO)P*(RFJ)P*(6OO)P*(6OO)P*(6NW))-3')


Mass: 6637.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 355 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 350 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.8 M Ammonium sulphate, 0.1 M citrate pH 4.0

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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: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.299→35.133 Å / Num. obs: 65937 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 12.67
Reflection shellResolution: 1.299→1.346 Å / Num. unique obs: 6385 / CC1/2: 0.397

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSvJan10,2014data reduction
Aimlessv0.7.4data scaling
PHASERv2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qk9

2qk9


Resolution: 1.299→35.133 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.83
RfactorNum. reflection% reflection
Rfree0.2286 3320 5.04 %
Rwork0.1895 --
obs0.1914 65928 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.01 Å2 / Biso mean: 23.5414 Å2 / Biso min: 11.22 Å2
Refinement stepCycle: final / Resolution: 1.299→35.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 439 53 350 2006
Biso mean--35.47 33.41 -
Num. residues----188
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2991-1.31770.34821360.3687246296
1.3177-1.33740.39581420.35032583100
1.3374-1.35830.33991400.33812562100
1.3583-1.38050.34641310.3252593100
1.3805-1.40430.30381470.31362570100
1.4043-1.42990.30321480.28912576100
1.4299-1.45740.29671240.28112580100
1.4574-1.48710.30851360.2622595100
1.4871-1.51950.28041370.23622585100
1.5195-1.55480.2371350.22332584100
1.5548-1.59370.26821360.21792586100
1.5937-1.63680.2711370.20582593100
1.6368-1.68490.21811370.18962608100
1.6849-1.73930.21431370.18162596100
1.7393-1.80150.20961370.17752619100
1.8015-1.87360.21541380.1852607100
1.8736-1.95890.2461370.20292611100
1.9589-2.06210.25821360.18892592100
2.0621-2.19130.21661390.1792636100
2.1913-2.36050.22111400.18042642100
2.3605-2.59790.23891390.18342649100
2.5979-2.97370.2261410.1822668100
2.9737-3.74590.19671410.15832696100
3.7459-35.1330.191490.15682815100

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