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- PDB-7xj4: Crystal structure of engineered HIV-1 Reverse Transcriptase RNase... -

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Basic information

Entry
Database: PDB / ID: 7xj4
TitleCrystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with nitrofuran methoxy(methoxycarbonyl)phenyl ester
ComponentsReverse Transcriptase RNase H domain
KeywordsVIRAL PROTEIN / ribonuclease
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / telomerase activity / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity ...RNA-directed DNA polymerase activity / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / telomerase activity / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral ...Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-E9B / : / Pol protein / Pol protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLu, H. / Komukai, Y. / Usami, K. / Guo, Y. / Qiao, X. / Nukaga, M. / Hoshino, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K07050 Japan
CitationJournal: J.Chem.Inf.Model. / Year: 2022
Title: Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds for HIV-1 RNase H Activity.
Authors: Lu, H. / Komukai, Y. / Usami, K. / Guo, Y. / Qiao, X. / Nukaga, M. / Hoshino, T.
History
DepositionApr 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reverse Transcriptase RNase H domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4987
Polymers16,8321
Non-polymers6656
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-45 kcal/mol
Surface area8270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.447, 60.447, 82.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Reverse Transcriptase RNase H domain


Mass: 16832.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pET50(b) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLys
References: UniProt: A0A059PIR4, UniProt: A0A7L9QW77, retroviral ribonuclease H
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-E9B / S-[5-[(E)-2-phenylethenyl]-1,3,4-oxadiazol-2-yl] 5-nitrothiophene-2-carbothioate


Mass: 359.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H9N3O4S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45 % / Mosaicity: 0.23 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.1M MES, 26%(v/v) PEG 6000, 0.01M Zinc Sulfate, 0.001M MANGANESE CHLORIDE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2022 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.74 Å / Num. obs: 27041 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 32.79 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.029 / Rrim(I) all: 0.103 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8411.31.68195308420.5740.5151.7611.699.7
9-48.749.70.07515881630.9860.0290.08133.199.9

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
XDSdata reduction
Aimless0.1.27data scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QIN

3qin


Resolution: 1.8→48.74 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 27.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 1349 4.99 %
Rwork0.2174 25692 -
obs0.2188 27041 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.71 Å2 / Biso mean: 40.4437 Å2 / Biso min: 20.98 Å2
Refinement stepCycle: final / Resolution: 1.8→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 29 16 1214
Biso mean--53.99 35.7 -
Num. residues----149
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.860.34721330.292925432676
1.86-1.940.22251310.247425702701
1.94-2.030.32591350.257225872722
2.03-2.130.25881360.216225582694
2.13-2.270.28951340.227625692703
2.27-2.440.25561360.21325802716
2.44-2.690.30231330.241725722705
2.69-3.080.26531350.241425712706
3.08-3.880.24831340.218525732707
3.88-48.740.18731420.189425692711

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