[English] 日本語
Yorodumi
- PDB-7o0h: Structure of the foamy viral protease-reverse transcriptase dRH i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o0h
TitleStructure of the foamy viral protease-reverse transcriptase dRH in complex with ds DNA.
Components
  • DNA (5'-D(*AP*AP*CP*AP*GP*AP*GP*TP*GP*CP*GP*AP*CP*AP*C)-3')
  • DNA (5'-D(*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


virion component / DNA integration / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / nucleic acid binding / aspartic-type endopeptidase activity ...virion component / DNA integration / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / nucleic acid binding / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / proteolysis / metal ion binding / cytoplasm
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 / RNase H ...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. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Pro-Pol polyprotein
Similarity search - Component
Biological speciesWhite-tufted-ear marmoset simian foamy virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsNowak, E. / Nowacka, M. / Nowotny, M.
Funding support Poland, 1items
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 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)143,2564
Polymers143,2564
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer upon binding dsDNa
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-25 kcal/mol
Surface area53230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.516, 107.558, 118.090
Angle α, β, γ (deg.)90.000, 98.720, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
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


Mass: 67342.812 Da / Num. of mol.: 2
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*C)-3')


Mass: 4612.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*CP*TP*G)-3')


Mass: 3958.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, DL malic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.09→50 Å / Num. obs: 35709 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 86.18 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.3
Reflection shellResolution: 3.09→3.28 Å / Num. unique obs: 5612 / CC1/2: 0.564

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MFV RT

Resolution: 3.09→48.84 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2853 1786 5 %
Rwork0.2298 33904 -
obs0.2326 35690 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 239.79 Å2 / Biso mean: 104.9667 Å2 / Biso min: 36.74 Å2
Refinement stepCycle: final / Resolution: 3.09→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8341 569 0 0 8910
Num. residues----1117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.09-3.180.34361300.34572457258795
3.18-3.270.39851370.341125992736100
3.27-3.380.41321370.335526102747100
3.38-3.50.36251370.299125952732100
3.5-3.640.32581370.276626122749100
3.64-3.80.31151380.268426212759100
3.8-40.31661370.243526012738100
4-4.250.28671380.20626102748100
4.25-4.580.2241380.184526302768100
4.58-5.040.24451380.187826242762100
5.04-5.770.27071380.209726242762100
5.77-7.270.25361400.23326482788100
7.27-48.840.26171410.19672673281499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.1297-1.4441-1.11926.94481.89492.3495-0.0772-0.8493-0.39860.5321-0.0415-1.0215-1.18591.12210.11661.0336-0.2702-0.32410.80480.2680.9968190.257915.4258123.3826
22.3479-0.9995-0.00983.3786-0.07143.0827-0.13740.18690.52810.1311-0.08910.5695-0.7085-0.2540.15670.70290.001-0.03750.3620.07210.9379166.24747.1044117.7609
32.4992-0.2676-1.05692.76340.06235.2309-0.0887-0.1420.22710.54340.11860.0942-0.5215-0.0441-0.00360.52220.0496-0.04950.27360.04770.7014165.1214-0.7892127.0043
41.71690.05080.15922.1646-1.163.8964-0.0681-0.5361-0.20010.56760.24470.2077-0.0521-0.7569-0.17340.72960.04980.22480.70990.12030.6442150.9021-21.9037148.2763
51.3561-0.4483-0.58432.0625-1.451.6662-0.13810.35370.05670.2901-0.9161-1.16650.09882.08760.98080.77040.1921-0.06611.58620.58091.5206201.5299-5.5814126.2051
60.8792-0.1005-0.771.2055-0.83832.1322-0.1338-0.6484-0.17530.5749-0.1668-0.3610.41280.81010.25440.96870.1742-0.21980.93690.18180.8913189.2627-28.7913154.5393
74.07063.4627-3.90039.4248-1.26744.37640.1986-0.0026-0.71660.29740.24380.95490.83220.1194-0.48160.6221-0.0578-0.15050.6530.05691.0372157.8942-25.9994129.1996
83.9572-1.38380.76455.52580.9142.23750.3251-0.0026-1.20.6019-0.21420.6710.7256-0.2425-0.15630.7887-0.2272-0.03450.65080.01460.973157.1942-25.3433131.6448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 75 )A5 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 202 )A76 - 202
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 357 )A203 - 357
4X-RAY DIFFRACTION4chain 'A' and (resid 358 through 571 )A358 - 571
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 104 )B3 - 104
6X-RAY DIFFRACTION6chain 'B' and (resid 105 through 578 )B105 - 578
7X-RAY DIFFRACTION7chain 'E' and (resid 1 through 15 )E1 - 15
8X-RAY DIFFRACTION8chain 'F' and (resid 1 through 13 )F1 - 13

+
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://pdbjlvh1.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