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- PDB-8swc: RNase H complex with ASO (OOO) and RNA -

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Basic information

Entry
Database: PDB / ID: 8swc
TitleRNase H complex with ASO (OOO) and RNA
Components
  • PO ASO
  • 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 OOO stereochemistry (PO-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
PHOSPHATE ION / DNA / DNA (> 10) / RNA / RNA (> 10) / Ribonuclease H1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 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/PO-ASO complex at an atomic level
Authors: Iwamoto, N. / Cho, Y.-J.
History
DepositionMay 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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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: PO ASO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6209
Polymers46,2143
Non-polymers4066
Water905
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 area8510 Å2
ΔGint-58 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.617, 100.617, 82.092
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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

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


Mass: 33218.457 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 PO ASO


Mass: 6380.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 11 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2:1 complex : precipitant (0.1 M sodium acetate, pH 4.6, 8% w/v PEG4000), cryoprotection: mother liquor + 25% v/v glycerol, 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: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.67→43.57 Å / Num. obs: 13859 / % possible obs: 98.9 % / Redundancy: 19.7 % / Biso Wilson estimate: 75.44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.016 / Rrim(I) all: 0.072 / Net I/σ(I): 30.2
Reflection shellResolution: 2.67→2.8 Å / Num. unique obs: 1677 / CC1/2: 0.871

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QK9

2qk9


Resolution: 2.68→38.48 Å / SU ML: 0.4417 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.449
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22 720 5.24 %
Rwork0.1915 13032 -
obs0.193 13752 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.64 Å2
Refinement stepCycle: LAST / Resolution: 2.68→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 772 107 5 2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032164
X-RAY DIFFRACTIONf_angle_d0.64893104
X-RAY DIFFRACTIONf_chiral_restr0.0371344
X-RAY DIFFRACTIONf_plane_restr0.0022253
X-RAY DIFFRACTIONf_dihedral_angle_d19.9028570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.890.35111310.30252548X-RAY DIFFRACTION98.53
2.89-3.180.35411300.28392594X-RAY DIFFRACTION99.71
3.18-3.640.27181660.23152552X-RAY DIFFRACTION99.89
3.64-4.580.19721560.18462621X-RAY DIFFRACTION100
4.58-38.480.17521370.15022717X-RAY DIFFRACTION99.86
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)
13.179869312252.76107332702-0.150544534945.54379903058-3.940135592634.522011618250.0929901787423-1.31318626955-0.5925960149430.667938811871-0.1580617616650.5569098356030.163392025928-0.3652470915630.03499870657590.780032699043-0.176592997702-0.03405897152240.69159143218-0.0748309043360.592602453462-63.497127390511.79586061521.27288667808
26.285147391861.36830358864-1.035695556865.894774766692.216922438685.99423123884-0.196906443602-0.186918121352-0.6916704151480.208207609086-0.200008957293-0.7260993111940.4372909130130.4539335706050.460986751380.8816757723290.0727953599519-0.01786787712540.5828196551760.09603460807410.716124780787-49.55506871249.15510292557-8.86733414277
34.38015317254-4.21573892119-0.5972345595054.534492173132.257933068086.557455110240.617019990940.160901294023-0.454759807302-0.0918226355075-0.41105642620.7441172993680.248259343713-0.796474949862-0.06780368783250.646744245609-0.138018215288-0.09071357616880.5723458669960.03172937811740.652065101574-62.290680614613.0223468269-6.74034935896
47.099423995294.07744924413-1.149537781297.83519767794-1.349452876835.406098368340.115046984019-0.3022014792060.318517047650.36095924763-0.1150705257040.351914792892-0.623223928676-0.4337517432350.0802733719140.6555448612680.007653182434120.06316070684990.662559557785-0.02581618513610.481730662229-58.129330812626.05969213210.801631626883
56.477335723512.185216599971.038124935056.64124320596-1.103166811088.48923804923-0.0948575815803-0.347360223820.332482048555-0.229447723040.05542309293740.7188582213940.0177990405355-1.358314132550.07003788425620.595015043713-0.02669887489770.02280927598370.617559745382-0.03914120274940.677413547685-62.523531449124.1236636128-2.00154257417
60.098920608533-0.129123182963-0.589261323041.29090032688-0.1625525577874.485223978010.8399992662280.7639949250422.37753194842-0.064892267890.5850269244491.611569931351.793039162540.945829926254-1.239218333340.899482019888-0.09426222908830.1342404491870.974914285903-0.005761244897171.30555580217-56.69267840857.009008918329.74943117528
75.95232012326-2.32714753658-6.526385162556.435506228920.9416584340088.41014032371-0.389791172727-0.393167462109-0.571230450271-0.0741508794828-0.2602771248830.6720688398091.535644322840.3451043892240.4270899515190.977905803731-0.222581000792-0.1274539284750.731537852904-0.01274535154710.780094413366-57.77288256944.02623737794-5.46067397545
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 138 through 149 )138 - 1491 - 12
22chain 'A' and (resid 150 through 163 )150 - 16313 - 26
33chain 'A' and (resid 164 through 199 )164 - 19927 - 62
44chain 'A' and (resid 200 through 238 )200 - 23863 - 101
55chain 'A' and (resid 239 through 260 )239 - 260102 - 123
66chain 'A' and (resid 261 through 267 )261 - 267124 - 130
77chain 'A' and (resid 268 through 286 )268 - 286131 - 149

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