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- EMDB-12698: Structure of the foamy viral protease-reverse transcriptase in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-12698
TitleStructure of the foamy viral protease-reverse transcriptase in complex with dsDNA.
Map data
Samplecomplex of protease-reverse transcriptase with ds DNA:
(Pr125Pol) x 2 / DNA / (nucleic-acidNucleic acid) x 2
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
Foamy virus protease (FV PR) domain profile. / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease A9 / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Integrase zinc binding domain / Integrase zinc-binding domain / RNase H-like domain found in reverse transcriptase / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H ...Foamy virus protease (FV PR) domain profile. / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease A9 / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Integrase zinc binding domain / Integrase zinc-binding domain / RNase H-like domain found in reverse transcriptase / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H / Integrase core domain / Integrase catalytic domain profile. / Integrase, catalytic core / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / 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
Biological speciesWhite-tufted-ear marmoset simian foamy virus / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsCzarnocki-Cieciura M
Funding support Poland, 1 items
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 RH / Woehrl BM / Nowotny M
History
DepositionMar 30, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateJun 30, 2021-
Current statusJun 30, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7o24
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12698.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 384 pix.
= 330.24 Å
0.86 Å/pix.
x 384 pix.
= 330.24 Å
0.86 Å/pix.
x 384 pix.
= 330.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.01831851 - 0.039614014
Average (Standard dev.)2.8691395e-05 (±0.0015421817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z330.240330.240330.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0180.0400.000

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Supplemental data

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Segmentation: #1

Fileemd_12698_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_12698_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_12698_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire complex of protease-reverse transcriptase with ds DNA

EntireName: complex of protease-reverse transcriptase with ds DNA / Number of Components: 6

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Component #1: protein, complex of protease-reverse transcriptase with ds DNA

ProteinName: complex of protease-reverse transcriptase with ds DNA / Recombinant expression: No
MassExperimental: 190 kDa

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Component #2: protein, Pr125Pol

ProteinName: Pr125Pol / Recombinant expression: No
SourceSpecies: White-tufted-ear marmoset simian foamy virus
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #3: protein, DNA

ProteinName: DNA / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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Component #4: protein, Pr125Pol

ProteinName: Pr125Pol
Details: NCBI Reference Sequence: NC_039030.1 TYG codon placed as LEU 586
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 85.467289 kDa
SourceSpecies: White-tufted-ear marmoset simian foamy virus
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #5: nucleic-acid, DNA (5'-D(*AP*AP*CP*AP*GP*AP*GP*TP*GP*CP*GP*AP*CP*A...

nucleic acidName: 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')
Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DA)(DC)(DA)(DG)(DA)(DG)(DT)(DG)(DC) (DG)(DA)(DC)(DA)(DC)(DC)(DT)(DG)(DA)(DT) (DT)(DC)(DC)(DA)
MassTheoretical: 7.34777 kDa
SourceSpecies: synthetic construct (others)

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Component #6: nucleic-acid, DNA (5'-D(*TP*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C...

nucleic acidName: 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')
Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DG)(DG)(DA)(DA)(DT)(DC)(DA)(DG)(DG) (DT)(DG)(DT)(DC)(DG)(DC)(DA)(DC)(DT)(DC) (DT)(DG)
MassTheoretical: 6.783375 kDa
SourceSpecies: synthetic construct (others)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / pH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 40 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 20071
3D reconstructionSoftware: RELION / Resolution: 4.8 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

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