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- PDB-9uoa: Crystal structure of HIV-1 Reverse Transcriptase RNase H domain c... -

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Basic information

Entry
Database: PDB / ID: 9uoa
TitleCrystal structure of HIV-1 Reverse Transcriptase RNase H domain complexed with a galloyl inhibitor
ComponentsReverse transcriptase/RNaseH
KeywordsVIRAL PROTEIN / Inhibitor / Complex / RNase
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis ...RNA-directed DNA polymerase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / identical protein binding / metal ion binding
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / : / Reverse transcriptase/RNaseH
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsWei, S. / Fujimoto, K. / Tang, K. / Zhan, P. / Menendez-Arias, L. / Hoshino, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Structural Analysis of HIV-1 RNase H bound to a Galloyl Active Site Inhibitor and Computational Compound Modification
Authors: Wei, S. / Fujimoto, K. / Tang, K. / Zhan, P. / Menendez-Arias, L. / Hoshino, T.
History
DepositionApr 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reverse transcriptase/RNaseH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4435
Polymers16,8321
Non-polymers6114
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-24 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.255, 61.255, 83.122
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 Reverse transcriptase/RNaseH


Mass: 16832.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET50(b) / Production host: Escherichia coli (E. coli) / References: UniProt: Q72547
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1L9C / ~{N}-[4-[4-[3,4,5-tris(oxidanyl)phenyl]carbonylpiperazin-1-yl]sulfonylphenyl]ethanamide


Mass: 435.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O7S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging 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: 0.98 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 23, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.96→43.31 Å / Num. obs: 11986 / % possible obs: 100 % / Redundancy: 24.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.017 / Rrim(I) all: 0.084 / Χ2: 1.22 / Net I/σ(I): 24 / Num. measured all: 288857
Reflection shellResolution: 1.96→2.01 Å / % possible obs: 100 % / Redundancy: 25.3 % / Rmerge(I) obs: 1.322 / Num. measured all: 20530 / Num. unique obs: 813 / CC1/2: 0.88 / Rpim(I) all: 0.264 / Rrim(I) all: 1.349 / Χ2: 0.83 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→43.31 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2816 1151 10 %
Rwork0.2505 --
obs0.2537 11512 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→43.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1154 0 33 39 1226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.078
X-RAY DIFFRACTIONf_dihedral_angle_d5.394169
X-RAY DIFFRACTIONf_chiral_restr0.041184
X-RAY DIFFRACTIONf_plane_restr0.007204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.050.39851410.32411276X-RAY DIFFRACTION98
2.05-2.150.42071220.36541101X-RAY DIFFRACTION84
2.16-2.290.35051330.35131193X-RAY DIFFRACTION90
2.29-2.470.32351470.27121319X-RAY DIFFRACTION100
2.47-2.720.31791450.26881311X-RAY DIFFRACTION99
2.72-3.110.29361500.27281344X-RAY DIFFRACTION100
3.11-3.910.27731510.23981360X-RAY DIFFRACTION100
3.92-43.310.23591620.21611457X-RAY DIFFRACTION100

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