[English] 日本語
Yorodumi
- EMDB-12698: Structure of the foamy viral protease-reverse transcriptase in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12698
TitleStructure of the foamy viral protease-reverse transcriptase in complex with dsDNA.
Map datasharpened with b-factor -134.373
Sample
  • Complex: complex of protease-reverse transcriptase with ds DNA
    • Complex: Pr125Pol
      • Protein or peptide: Pr125Pol
    • Complex: DNA
      • DNA: 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: 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')
Keywordsreverse trancscriptase / complex with dsDNA / VIRAL PROTEIN
Function / homology
Function and homology information


DNA integration / virion component / viral genome integration into host DNA / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA-DNA hybrid ribonuclease activity / host cell / DNA recombination / aspartic-type endopeptidase activity ...DNA integration / virion component / viral genome integration into host DNA / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA-DNA hybrid ribonuclease activity / host cell / DNA recombination / aspartic-type endopeptidase activity / nucleic acid binding / host cell cytoplasm / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / proteolysis / metal ion binding
Similarity search - Function
Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / 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 ...Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / 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. / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like 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: J Virol / Year: 2021
Title: Structures of Substrate Complexes of Foamy Viral Protease-Reverse Transcriptase.
Authors: Marzena Nowacka / Elżbieta Nowak / Mariusz Czarnocki-Cieciura / Justyna Jackiewicz / Krzysztof Skowronek / Roman H Szczepanowski / Birgitta M Wöhrl / Marcin Nowotny /
Abstract: Reverse transcriptases (RTs) use their DNA polymerase and RNase H activities to catalyze the conversion of single-stranded RNA to double-stranded DNA (dsDNA), a crucial process for the replication of ...Reverse transcriptases (RTs) use their DNA polymerase and RNase H activities to catalyze the conversion of single-stranded RNA to double-stranded DNA (dsDNA), a crucial process for the replication of retroviruses. Foamy viruses (FVs) possess a unique RT, which is a fusion with the protease (PR) domain. The mechanism of substrate binding by this enzyme has been unknown. Here, we report a crystal structure of monomeric full-length marmoset FV (MFV) PR-RT in complex with an RNA/DNA hybrid substrate. We also describe a structure of MFV PR-RT with an RNase H deletion in complex with a dsDNA substrate in which the enzyme forms an asymmetric homodimer. Cryo-electron microscopy reconstruction of the full-length MFV PR-RT-dsDNA complex confirmed the dimeric architecture. These findings represent the first structural description of nucleic acid binding by a foamy viral RT and demonstrate its ability to change its oligomeric state depending on the type of bound nucleic acid. Reverse transcriptases (RTs) are intriguing enzymes converting single-stranded RNA to dsDNA. Their activity is essential for retroviruses, which are divided into two subfamilies differing significantly in their life cycles: and . The latter family is much more ancient and comprises five genera. A unique feature of foamy viral RTs is that they contain N-terminal protease (PR) domains, which are not present in orthoretroviral enzymes. So far, no structural information for full-length foamy viral PR-RT interacting with nucleic substrates has been reported. Here, we present crystal and cryo-electron microscopy structures of marmoset foamy virus (MFV) PR-RT. These structures revealed the mode of binding of RNA/DNA and dsDNA substrates. Moreover, unexpectedly, the structures and biochemical data showed that foamy viral PR-RT can adopt both a monomeric configuration, which is observed in our structures in the presence of an RNA/DNA hybrid, and an asymmetric dimer arrangement, which we observed in the presence of dsDNA.
History
DepositionMar 30, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
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
  • Download
  • 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

emd_12698.png

Downloads & links

-
Map

FileDownload / File: emd_12698.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened with b-factor -134.373
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.01831851 - 0.039614014
Average (Standard dev.)0.000028691395 (±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

-
Supplemental data

-
Mask #1

Fileemd_12698_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_12698_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_12698_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : complex of protease-reverse transcriptase with ds DNA

EntireName: complex of protease-reverse transcriptase with ds DNA
Components
  • Complex: complex of protease-reverse transcriptase with ds DNA
    • Complex: Pr125Pol
      • Protein or peptide: Pr125Pol
    • Complex: DNA
      • DNA: 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: 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')

-
Supramolecule #1: complex of protease-reverse transcriptase with ds DNA

SupramoleculeName: complex of protease-reverse transcriptase with ds DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 190 KDa

-
Supramolecule #2: Pr125Pol

SupramoleculeName: Pr125Pol / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: White-tufted-ear marmoset simian foamy virus

-
Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: synthetic construct (others)

-
Macromolecule #1: Pr125Pol

MacromoleculeName: Pr125Pol / type: protein_or_peptide / ID: 1
Details: NCBI Reference Sequence: NC_039030.1 TYG codon placed as LEU 586
Number of copies: 3 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: White-tufted-ear marmoset simian foamy virus
Molecular weightTheoretical: 85.467289 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MTTPPLLQLP VEVKKTELNG FWDTGAQITC IPEAFLKEEI PIGEAQIKTL HGTKLQSVYY LKFKVLGRKV EAEVTTSPFD YVIISPSDI PWYKPQPLEL TVKLPVQDFK KELINKANIN NEEKKQLAKL LDKYDVLWQQ WENQVGHRKI PPHNIATGTV A PRPQRQYH ...String:
MTTPPLLQLP VEVKKTELNG FWDTGAQITC IPEAFLKEEI PIGEAQIKTL HGTKLQSVYY LKFKVLGRKV EAEVTTSPFD YVIISPSDI PWYKPQPLEL TVKLPVQDFK KELINKANIN NEEKKQLAKL LDKYDVLWQQ WENQVGHRKI PPHNIATGTV A PRPQRQYH INTKAKPSIQ QVIDDLLKQG VLIKQTSVMN TPIYPVPKPD GKWRMVLDYR AVNKTVPLIG AQNQHSLGIL TN LVRQKYK STIDLSNGFW AHPITKDSQW ITAFTWEGKQ HVWTRLPQGF LNSPALFTAD VVDLLKNIPG ISVYVDDIYF STE TVSEHL KILEKVFKIL LEAGYIVSLK KSALLRYEVT FLGFSITQTG RGLTSEFKDK IQNITSPRTL KELQSILGLF NFAR NFVPN FSEIIKPLYS LISTAEGNNI KWTSEHTRYL EEIVSALNHA GNLEQRDNES PLVVKLNASP KTGYIRYYNK GGQKP IAYA SHVFTNTELK FTPLEKLLVT MHKALIKAID LALGQPIEVY SPIISMQKLQ KTPLPERKAL STRWITWLSY LEDPRI TFY YDKTLPDLKN VPETVTDKKP KMLPIIEYAA VFYTDGSAIR SPDKNKSHSS GMGIVHAVFK PELTIEHQWS IPLGDHT AQ YAEISAVEFA CKKANNISGP VLIVTDSDYV ARSVNEELPF WRSNGFVNNK KKPLKHISKW KNISDSLLLK RDIIIVHE P GHKPSYTSIH TQGNNLADKL ATQGSYTVNN I

UniProtKB: Pro-Pol polyprotein

-
Macromolecule #2: DNA (5'-D(*AP*AP*CP*AP*GP*AP*GP*TP*GP*CP*GP*AP*CP*AP*CP*CP*TP*GP*...

MacromoleculeName: 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')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 7.34777 KDa
SequenceString:
(DA)(DA)(DC)(DA)(DG)(DA)(DG)(DT)(DG)(DC) (DG)(DA)(DC)(DA)(DC)(DC)(DT)(DG)(DA)(DT) (DT)(DC)(DC)(DA)

-
Macromolecule #3: DNA (5'-D(*TP*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*...

MacromoleculeName: 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')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.783375 KDa
SequenceString:
(DT)(DG)(DG)(DA)(DA)(DT)(DC)(DA)(DG)(DG) (DT)(DG)(DT)(DC)(DG)(DC)(DA)(DC)(DT)(DC) (DT)(DG)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 344421
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 20071
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7o24:
Structure of the foamy viral protease-reverse transcriptase in complex with dsDNA.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more