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- PDB-6dtw: HIV-1 Reverse Transcriptase Y181C Mutant in complex with JLJ 578 -

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Basic information

Entry
Database: PDB / ID: 6dtw
TitleHIV-1 Reverse Transcriptase Y181C Mutant in complex with JLJ 578
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsHYDROLASE / TRANSFERASE/INHIBITOR / HIV-1 / reverse transcriptase / inhibitor / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / 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. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / 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. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-H9Y / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.742 Å
AuthorsSasaki, T. / Gannam, Z.T.K. / Anderson, K.S. / Jorgensen, W.L. / Lee, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM049551 United States
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Molecular and cellular studies evaluating a potent 2-cyanoindolizine catechol diether NNRTI targeting wildtype and Y181C mutant HIV-1 reverse transcriptase.
Authors: Sasaki, T. / Gannam, Z.T.K. / Kudalkar, S.N. / Frey, K.M. / Lee, W.G. / Spasov, K.A. / Jorgensen, W.L. / Anderson, K.S.
History
DepositionJun 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reverse transcriptase/ribonuclease H
B: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5135
Polymers113,9692
Non-polymers5453
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-48 kcal/mol
Surface area46930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.289, 73.899, 108.249
Angle α, β, γ (deg.)90.00, 99.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Reverse transcriptase/ribonuclease H / p66 RT


Mass: 63929.207 Da / Num. of mol.: 1 / Mutation: C282S, K175A, K174A, Y181C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: gag-pol / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein p51 RT


Mass: 50039.488 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: gag-pol / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P03366

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Non-polymers , 4 types, 32 molecules

#3: Chemical ChemComp-H9Y / 8-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-6-fluoroindolizine-2-carbonitrile


Mass: 424.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C21H14F2N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: MES, PEG 8000, spermine, magnesium sulfate, ammonium sulfate, rilpivirine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.74→34.903 Å / Num. obs: 32884 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rsym value: 0.099 / Net I/σ(I): 30.1
Reflection shellResolution: 2.74→2.79 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1649 / Rsym value: 0.476 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
PHASERphasing
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MFB

4mfb


Resolution: 2.742→34.903 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.41
RfactorNum. reflection% reflection
Rfree0.2844 2000 6.08 %
Rwork0.2416 --
obs0.2442 32873 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.742→34.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7749 0 37 29 7815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027995
X-RAY DIFFRACTIONf_angle_d0.46610872
X-RAY DIFFRACTIONf_dihedral_angle_d9.4184807
X-RAY DIFFRACTIONf_chiral_restr0.0411178
X-RAY DIFFRACTIONf_plane_restr0.0041369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7422-2.81080.36471400.30692164X-RAY DIFFRACTION98
2.8108-2.88670.33591430.28212213X-RAY DIFFRACTION100
2.8867-2.97160.3471460.27452255X-RAY DIFFRACTION100
2.9716-3.06750.33281430.27832195X-RAY DIFFRACTION100
3.0675-3.17710.3551450.27562242X-RAY DIFFRACTION100
3.1771-3.30420.40141430.27242217X-RAY DIFFRACTION100
3.3042-3.45440.32981450.26262231X-RAY DIFFRACTION100
3.4544-3.63640.30981440.26392207X-RAY DIFFRACTION100
3.6364-3.86390.27241450.25082245X-RAY DIFFRACTION99
3.8639-4.16180.24821430.22722203X-RAY DIFFRACTION98
4.1618-4.57980.281400.21532159X-RAY DIFFRACTION97
4.5798-5.24060.21031420.22452214X-RAY DIFFRACTION97
5.2406-6.59530.2791440.24562217X-RAY DIFFRACTION99
6.5953-34.9060.27491370.22092111X-RAY DIFFRACTION91

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