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- PDB-8jyj: Crystal structure of engineered HIV-1 Reverse Transcriptase RNase... -

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Basic information

Entry
Database: PDB / ID: 8jyj
TitleCrystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with laccaic acid A
ComponentsPol protein,Pol protein,HIV-1 Reverse Transcriptase RNase H active domain
KeywordsVIRAL PROTEIN / Inhibitor
Function / homology
Function and homology information


DNA integration / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / peptidase activity / DNA recombination / nucleic acid binding / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis ...DNA integration / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / peptidase activity / DNA recombination / nucleic acid binding / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding / metal ion binding
Similarity search - Function
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 ...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. / RNase H type-1 domain profile. / Ribonuclease H domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / Chem-VA9 / Pol protein / Pol protein
Similarity search - Component
Biological speciesHIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsIto, Y. / Lu, H. / Kitajima, M. / Ishikawa, H. / Nakata, Y. / Iwatani, Y. / Hoshino, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Nat.Prod. / Year: 2023
Title: Sticklac-Derived Natural Compounds Inhibiting RNase H Activity of HIV-1 Reverse Transcriptase.
Authors: Ito, Y. / Lu, H. / Kitajima, M. / Ishikawa, H. / Nakata, Y. / Iwatani, Y. / Hoshino, T.
History
DepositionJul 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pol protein,Pol protein,HIV-1 Reverse Transcriptase RNase H active domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6106
Polymers16,8321
Non-polymers7785
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.836, 61.836, 83.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Pol protein,Pol protein,HIV-1 Reverse Transcriptase RNase H active domain


Mass: 16832.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 06TG.HT008 (virus) / Gene: pol
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A059PIR4, UniProt: A0A1D9J5E8, retroviral ribonuclease H
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-VA9 / 7-[5-(2-acetamidoethyl)-2-oxidanyl-phenyl]-3,5,6,8-tetrakis(oxidanyl)-9,10-bis(oxidanylidene)anthracene-1,2-dicarboxylic acid


Mass: 537.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H19NO12 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.1M MES, 26%(v/v) PEG6000, 0.01 M Zinc Sulfate, 0.001 M 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 4M / Detector: PIXEL / Date: Jun 27, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→43.72 Å / Num. obs: 11427 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.02 / Rrim(I) all: 0.07 / Net I/σ(I): 16.6 / Num. measured all: 144092
Reflection shellResolution: 2.01→2.06 Å / % possible obs: 98.9 % / Redundancy: 11.6 % / Rmerge(I) obs: 1.373 / Num. measured all: 9343 / Num. unique obs: 807 / CC1/2: 0.749 / Rpim(I) all: 0.416 / Rrim(I) all: 1.437 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→43.72 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2977 1087 10.08 %
Rwork0.2431 --
obs0.2483 10786 94.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1131 0 43 23 1197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.953
X-RAY DIFFRACTIONf_dihedral_angle_d3.933161
X-RAY DIFFRACTIONf_chiral_restr0.038181
X-RAY DIFFRACTIONf_plane_restr0.005202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.10.42381100.3928996X-RAY DIFFRACTION80
2.1-2.210.3471290.31131155X-RAY DIFFRACTION92
2.21-2.350.34981310.29481127X-RAY DIFFRACTION91
2.35-2.530.311380.30251217X-RAY DIFFRACTION96
2.53-2.780.31111390.28781239X-RAY DIFFRACTION98
2.78-3.180.31861420.29011273X-RAY DIFFRACTION99
3.19-4.010.28981430.2331300X-RAY DIFFRACTION100
4.01-43.720.27341550.20541392X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.1106 Å / Origin y: 14.3095 Å / Origin z: 14.9507 Å
111213212223313233
T0.3607 Å20.0125 Å2-0.0427 Å2-0.2607 Å20.0658 Å2--0.3637 Å2
L2.5126 °2-0.5976 °2-0.0036 °2-4.921 °21.2838 °2--3.7346 °2
S0.0483 Å °0.0089 Å °-0.2789 Å °0.0401 Å °-0.0326 Å °-0.2393 Å °0.0814 Å °-0.1899 Å °-0.0804 Å °
Refinement TLS groupSelection details: all

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