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- PDB-6ujy: HIV-1 wild-type reverse transcriptase-DNA complex with (-)-3TC-TP -

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Basic information

Entry
Database: PDB / ID: 6ujy
TitleHIV-1 wild-type reverse transcriptase-DNA complex with (-)-3TC-TP
Components
  • p51 Reverse transcriptase/RNaseH
  • p66 Reverse transcriptase/RNaseH
  • primer DNA
  • template DNA
KeywordsVIRAL PROTEIN / HIV-1 reverse transcriptase NRTI polymerase DNA complex
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host multivesicular body / protein processing / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / zinc ion binding / identical protein 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal 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. / 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. / Aspartic peptidase domain superfamily / Ribonuclease H 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
Lamivudine Triphosphate / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59456090099 Å
AuthorsLansdon, E.B.
CitationJournal: Commun Biol / Year: 2019
Title: Elucidating molecular interactions ofL-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance.
Authors: Hung, M. / Tokarsky, E.J. / Lagpacan, L. / Zhang, L. / Suo, Z. / Lansdon, E.B.
History
DepositionOct 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: p66 Reverse transcriptase/RNaseH
B: p51 Reverse transcriptase/RNaseH
P: primer DNA
T: template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7648
Polymers132,0794
Non-polymers6864
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-72 kcal/mol
Surface area45730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.702, 169.479, 102.766
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-804-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein p66 Reverse transcriptase/RNaseH / Exoribonuclease H / p66 RT


Mass: 65887.328 Da / Num. of mol.: 1 / Mutation: Q845C,C867S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein p51 Reverse transcriptase/RNaseH / Exoribonuclease H / p51 RT


Mass: 51382.984 Da / Num. of mol.: 1 / Mutation: C867S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H

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DNA chain , 2 types, 2 molecules PT

#3: DNA chain primer DNA


Mass: 6360.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: DNA chain template DNA


Mass: 8448.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1

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Non-polymers , 4 types, 193 molecules

#5: Chemical ChemComp-1RZ / Lamivudine Triphosphate / Lamivudine-5'-triphosphate / 3TC Triphosphate / [[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 469.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N3O12P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2% PEG 4000, 100mM MES pH 6.0, 10mM magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97395 Å / Relative weight: 1
ReflectionResolution: 2.59456→50 Å / Num. obs: 45025 / % possible obs: 99.7 % / Redundancy: 4 % / Biso Wilson estimate: 40.7332583871 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.5
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.497 / Num. unique obs: 2238

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KK1

3kk1


Resolution: 2.59456090099→47.4573444442 Å / SU ML: 0.312528286529 / Cross valid method: THROUGHOUT / σ(F): 1.33556055346 / Phase error: 26.0151723808
RfactorNum. reflection% reflection
Rfree0.233541891499 3363 4.79914377453 %
Rwork0.177288485104 --
obs0.17995419765 41844 80.4766006316 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.9837094387 Å2
Refinement stepCycle: LAST / Resolution: 2.59456090099→47.4573444442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7709 820 38 189 8756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009425987902518893
X-RAY DIFFRACTIONf_angle_d1.1861219826112250
X-RAY DIFFRACTIONf_chiral_restr0.04754614018051333
X-RAY DIFFRACTIONf_plane_restr0.006306749920811391
X-RAY DIFFRACTIONf_dihedral_angle_d18.32828675413413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5946-2.63160.379284856387540.2344306011256X-RAY DIFFRACTION36.2378976487
2.6316-2.67090.355168626347830.215576070161509X-RAY DIFFRACTION43.4616434616
2.6709-2.71260.350423527643770.2253907913091661X-RAY DIFFRACTION48.3449235049
2.7126-2.75710.3130263036661050.2378490012861820X-RAY DIFFRACTION52.2813688213
2.7571-2.80460.324897889119990.2293281283741991X-RAY DIFFRACTION58.1363004172
2.8046-2.85560.3045743140081120.2508471644092173X-RAY DIFFRACTION63.0170987314
2.8556-2.91050.2828397867411150.2389145656122370X-RAY DIFFRACTION68.4007707129
2.9105-2.96990.3127814643431300.2343622410782465X-RAY DIFFRACTION71.4285714286
2.9699-3.03450.3176512742811250.2345723343892586X-RAY DIFFRACTION75.4942912838
3.0345-3.10510.2751905032631500.2339085539722778X-RAY DIFFRACTION80.5723720418
3.1051-3.18270.2809080201041530.2224705586192913X-RAY DIFFRACTION84.6026490066
3.1827-3.26880.286969591151560.2104750918233021X-RAY DIFFRACTION87.4724669604
3.2688-3.36490.2356228336491580.1952063960523107X-RAY DIFFRACTION90.5184363737
3.3649-3.47350.2366640148511540.1923947130193243X-RAY DIFFRACTION93.017524644
3.4735-3.59760.2547571751131630.1912017185663270X-RAY DIFFRACTION94.4689047881
3.5976-3.74160.2640220304881640.1819940240063341X-RAY DIFFRACTION96.9303097345
3.7416-3.91180.2556356272071710.1694714953613353X-RAY DIFFRACTION97.8073827366
3.9118-4.11790.2036764123531710.1545673726913457X-RAY DIFFRACTION98.8825292995
4.1179-4.37580.1901804227881810.1424585993423399X-RAY DIFFRACTION99.1140642303
4.3758-4.71330.1976250210761570.1413321915823393X-RAY DIFFRACTION97.6884975234
4.7133-5.18710.2094201332311700.136176853483428X-RAY DIFFRACTION99.3099641181
5.1871-5.93650.2342500224971710.1557045104013421X-RAY DIFFRACTION99.1443555065
5.9365-7.47470.1725987483731790.1690999224793397X-RAY DIFFRACTION98.4310487201
7.4747-47.45730.1743312648321650.1604678749863360X-RAY DIFFRACTION96.9471947195

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