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

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Basic information

Entry
Database: PDB / ID: 8jyh
TitleCrystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with laccaic acid C
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-V96 / Pol protein / Pol protein
Similarity search - Component
Biological speciesHIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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)17,6126
Polymers16,8321
Non-polymers7805
Water19811
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)61.850, 61.850, 82.337
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-V96 / 7-[5-[(2~{S})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]-2-oxidanyl-phenyl]-3,5,6,8-tetrakis(oxidanyl)-9,10-bis(oxidanylidene)anthracene-1,2-dicarboxylic acid


Mass: 539.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H17NO13 / 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.: 11 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
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: 2.21→43.73 Å / Num. obs: 8440 / % possible obs: 99.7 % / Redundancy: 12.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.035 / Rrim(I) all: 0.12 / Net I/σ(I): 9.3 / Num. measured all: 106977
Reflection shellResolution: 2.21→2.29 Å / % possible obs: 97.2 % / Redundancy: 12.8 % / Rmerge(I) obs: 1.293 / Num. measured all: 9360 / Num. unique obs: 730 / CC1/2: 0.735 / Rpim(I) all: 0.372 / Rrim(I) all: 1.346 / Net I/σ(I) obs: 1.4

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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: 2.21→43.73 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 787 9.98 %
Rwork0.2278 --
obs0.2335 7885 93.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1125 0 43 11 1179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.382
X-RAY DIFFRACTIONf_dihedral_angle_d6.258160
X-RAY DIFFRACTIONf_chiral_restr0.058179
X-RAY DIFFRACTIONf_plane_restr0.007202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.350.3761180.3041025X-RAY DIFFRACTION84
2.35-2.530.38171210.30521068X-RAY DIFFRACTION88
2.53-2.790.37591280.28531166X-RAY DIFFRACTION93
2.79-3.190.27191280.29441211X-RAY DIFFRACTION97
3.19-4.020.34991380.24221267X-RAY DIFFRACTION99
4.02-43.730.23151540.18871361X-RAY DIFFRACTION100

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