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- PDB-7o24: Structure of the foamy viral protease-reverse transcriptase in co... -

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Basic information

Entry
Database: PDB / ID: 7o24
TitleStructure of the foamy viral protease-reverse transcriptase in complex with dsDNA.
Components
  • DNA (5'-D(*AP*AP*CP*AP*GP*AP*GP*TP*GP*CP*GP*AP*CP*AP*CP*CP*TP*GP*AP*TP*TP*CP*CP*A)-3')
  • DNA (5'-D(*TP*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*CP*TP*G)-3')
  • Pr125Pol
KeywordsVIRAL PROTEIN / reverse trancscriptase / complex with dsDNA
Function / homology
Function and homology information


ribonuclease H / DNA integration / viral penetration into host nucleus / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity ...ribonuclease H / DNA integration / viral penetration into host nucleus / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / host cell cytoplasm / host cell nucleus / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Spumavirus aspartic protease (A9) / Foamy virus protease (FV PR) domain profile. / Retroviral integrase, C-terminal SH3 domain / Retroviral integrase C-terminal SH3 domain / Spumavirus aspartic protease A9 / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / RNase H ...Spumavirus aspartic protease (A9) / Foamy virus protease (FV PR) domain profile. / Retroviral integrase, C-terminal SH3 domain / Retroviral integrase C-terminal SH3 domain / Spumavirus aspartic protease A9 / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Pr125Pol
Similarity search - Component
Biological speciesWhite-tufted-ear marmoset simian foamy virus
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsNowotny, M. / Czarnocki-Cieciura, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2016/21/B/NZ1/02757 Poland
CitationJournal: To Be Published
Title: Crystal structures of foamy viral protease-reverse transcriptase reveal switching between monomeric and dimeric protein forms during reverse transcription
Authors: Nowacka, M. / Nowak, E. / Czarnocki-Cieciura, M. / Jackiewicz, J. / Skowronek, K. / Szczepanowski, R.H. / Woehrl, B.M. / Nowotny, M.
History
DepositionMar 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release

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Structure visualization

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  • Deposited structure unit
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Pr125Pol
B: Pr125Pol
C: Pr125Pol
E: DNA (5'-D(*AP*AP*CP*AP*GP*AP*GP*TP*GP*CP*GP*AP*CP*AP*CP*CP*TP*GP*AP*TP*TP*CP*CP*A)-3')
F: DNA (5'-D(*TP*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*CP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)270,5335
Polymers270,5335
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Dimer is formed upon binding dsDNA
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9020 Å2
ΔGint-33 kcal/mol
Surface area64530 Å2
MethodPISA

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Components

#1: Protein Pr125Pol / Pro-Pol polyprotein / Protease/Reverse transcriptase / Protease/Reverse transcriptase/ribonuclease ...Pro-Pol polyprotein / Protease/Reverse transcriptase / Protease/Reverse transcriptase/ribonuclease H / Ribonuclease H / p42In / p65Pro-RT / p87Pro-RT-RNaseH / Reverse transcriptase


Mass: 85467.289 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: foamy virus
Source: (gene. exp.) White-tufted-ear marmoset simian foamy virus
Gene: pol
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D5JWV1, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: DNA chain DNA (5'-D(*AP*AP*CP*AP*GP*AP*GP*TP*GP*CP*GP*AP*CP*AP*CP*CP*TP*GP*AP*TP*TP*CP*CP*A)-3')


Mass: 7347.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*CP*TP*G)-3')


Mass: 6783.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1complex of protease-reverse transcriptase with ds DNACOMPLEX#1-#30MULTIPLE SOURCES
2Pr125PolCOMPLEX#11RECOMBINANT
3DNACOMPLEX#2-#31RECOMBINANT
Molecular weightValue: 0.19 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12White-tufted-ear marmoset simian foamy virus2170205
23synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
23synthetic construct (others)32630
Buffer solutionpH: 7
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EPU2.8.1image acquisition
19RELION3.1particle selectiontemplate-based
20CTFFIND4.1CTF correction
21RELION3.1initial Euler assignment
22RELION3.1final Euler assignment
24RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 344421
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20071 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039685
ELECTRON MICROSCOPYf_angle_d0.58613406
ELECTRON MICROSCOPYf_dihedral_angle_d15.6551607
ELECTRON MICROSCOPYf_chiral_restr0.0411551
ELECTRON MICROSCOPYf_plane_restr0.0041539

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