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- PDB-8r0s: Structure of reverse transcriptase from Cauliflower Mosaic Virus ... -

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Basic information

Entry
Database: PDB / ID: 8r0s
TitleStructure of reverse transcriptase from Cauliflower Mosaic Virus in complex with RNA/DNA hybrid
Components
  • DNA (5'-D(*GP*CP*TP*AP*CP*GP*CP*AP*CP*TP*GP*CP*TP*GP*GP*A)-3')
  • Enzymatic polyprotein
  • RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*AP*GP*UP*GP*CP*GP*UP*AP*GP*C)-3')
KeywordsVIRAL PROTEIN / Reverse transcriptase / protein-RNA-DNA complex
Function / homology
Function and homology information


RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / endonuclease activity / proteolysis
Similarity search - Function
Peptidase A3A, cauliflower mosaic virus-type / Reverse transcriptase, RNase H-like domain / Cauliflower mosaic virus peptidase (A3) / RNase H-like domain found in reverse transcriptase / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Enzymatic polyprotein
Similarity search - Component
Biological speciesCauliflower mosaic virus
synthetic gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPrabaharan, C. / Figiel, M. / Chamera, S. / Szczepanowski, R. / Nowak, E. / Nowotny, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2016/21/B/NZ1/02757 Poland
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural and biochemical characterization of cauliflower mosaic virus reverse transcriptase.
Authors: Prabaharan, C. / Figiel, M. / Szczepanowski, R.H. / Skowronek, K. / Zajko, W. / Thangaraj, V. / Chamera, S. / Nowak, E. / Nowotny, M.
History
DepositionOct 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enzymatic polyprotein
C: RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*AP*GP*UP*GP*CP*GP*UP*AP*GP*C)-3')
D: DNA (5'-D(*GP*CP*TP*AP*CP*GP*CP*AP*CP*TP*GP*CP*TP*GP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)77,4983
Polymers77,4983
Non-polymers00
Water1,33374
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)88.820, 140.520, 52.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Enzymatic polyprotein


Mass: 67140.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cauliflower mosaic virus / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2D2PYL0, RNA-directed DNA polymerase
#2: RNA chain RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*AP*GP*UP*GP*CP*GP*UP*AP*GP*C)-3')


Mass: 5458.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic gene (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*AP*CP*GP*CP*AP*CP*TP*GP*CP*TP*GP*GP*A)-3')


Mass: 4899.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic gene (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.04M Citric acid, 0.06M Bis-Tris propane , 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03234 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Dec 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03234 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 28172 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 58.97 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.3
Reflection shellResolution: 2.35→2.49 Å / Num. unique obs: 4464 / CC1/2: 0.478

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→45.25 Å / SU ML: 0.3858 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4665
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2631 1408 5 %
Rwork0.2143 26755 -
obs0.2168 28163 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.44 Å2
Refinement stepCycle: LAST / Resolution: 2.35→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3655 675 0 74 4404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084499
X-RAY DIFFRACTIONf_angle_d1.01036249
X-RAY DIFFRACTIONf_chiral_restr0.0535712
X-RAY DIFFRACTIONf_plane_restr0.0075684
X-RAY DIFFRACTIONf_dihedral_angle_d10.6741847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.38211360.35182600X-RAY DIFFRACTION99.6
2.43-2.530.42531390.3142646X-RAY DIFFRACTION99.89
2.53-2.650.32641390.2722635X-RAY DIFFRACTION99.86
2.65-2.790.37711400.25412650X-RAY DIFFRACTION100
2.79-2.960.31621380.26772633X-RAY DIFFRACTION99.96
2.96-3.190.32691400.24832655X-RAY DIFFRACTION100
3.19-3.510.32171410.22722679X-RAY DIFFRACTION99.65
3.51-4.020.24571410.20082685X-RAY DIFFRACTION100
4.02-5.060.18671430.17272711X-RAY DIFFRACTION99.93
5.06-45.250.23821510.19362861X-RAY DIFFRACTION99.77

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