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- PDB-6uk0: HIV-1 M184V reverse transcriptase-DNA complex -

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Basic information

Entry
Database: PDB / ID: 6uk0
TitleHIV-1 M184V reverse transcriptase-DNA complex
Components
  • Primer DNA
  • Template DNA
  • p51 Reverse transcriptase/RNaseH
  • p66 Reverse transcriptase/RNaseH
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 / 2-LTR circle formation / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 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 / 2-LTR circle formation / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 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 / Assembly Of The HIV Virion / exoribonuclease H activity / Budding and maturation of HIV virion / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / telomerase activity / RNA stem-loop binding / 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 / viral translational frameshifting / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / 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. / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain 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. / 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
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: 2.75695227845 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)132,3278
Polymers132,0154
Non-polymers3124
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13010 Å2
ΔGint-101 kcal/mol
Surface area45000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.982, 169.682, 97.368
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

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein p66 Reverse transcriptase/RNaseH / Pr160Gag-Pol


Mass: 65855.258 Da / Num. of mol.: 1 / Mutation: M771V, 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 / Pr160Gag-Pol


Mass: 51350.922 Da / Num. of mol.: 1 / Mutation: M771V, 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 , 3 types, 25 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.25 %
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: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 35981 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 50.7244547399 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.1
Reflection shellResolution: 2.75→2.8 Å / Rmerge(I) obs: 0.491 / Num. unique obs: 3384

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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: 3KJV

3kjv


Resolution: 2.75695227845→48.684 Å / SU ML: 0.300385566354 / Cross valid method: THROUGHOUT / σ(F): 1.33386278276 / Phase error: 28.9521005926
RfactorNum. reflection% reflection
Rfree0.260070513973 1992 5.53979642917 %
Rwork0.205004944875 33966 -
obs0.208076918245 35958 99.156187955 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.437482959 Å2
Refinement stepCycle: LAST / Resolution: 2.75695227845→48.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7472 778 16 21 8287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01042970514758547
X-RAY DIFFRACTIONf_angle_d1.2549046869611762
X-RAY DIFFRACTIONf_chiral_restr0.05386416387711287
X-RAY DIFFRACTIONf_plane_restr0.006924620611731347
X-RAY DIFFRACTIONf_dihedral_angle_d19.03142133483275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.757-2.82590.3272055314771260.2491419542622171X-RAY DIFFRACTION90.3263861581
2.8259-2.90230.3381852165271390.2470340602792438X-RAY DIFFRACTION99.8450213096
2.9023-2.98770.3245517259341440.2448169162812398X-RAY DIFFRACTION99.8036906164
2.9877-3.08410.3538054257651400.2424945315532420X-RAY DIFFRACTION99.7273081418
3.0841-3.19430.2746572352991360.2250749629062400X-RAY DIFFRACTION100
3.1943-3.32220.2552474524011440.2143234432422437X-RAY DIFFRACTION99.7680711249
3.3222-3.47330.2892887973881470.2130310976192421X-RAY DIFFRACTION99.961074348
3.4733-3.65640.3027726621411430.2174761001282427X-RAY DIFFRACTION99.9222395023
3.6564-3.88540.2763262353191440.2016510922242444X-RAY DIFFRACTION100
3.8854-4.18520.2477480263751360.1883623019662430X-RAY DIFFRACTION99.9221183801
4.1852-4.60610.2326034655581490.1839108869532459X-RAY DIFFRACTION99.9233716475
4.6061-5.27190.2197935732031480.1761758424532454X-RAY DIFFRACTION99.808208669
5.2719-6.63940.234770475891500.2073230376532487X-RAY DIFFRACTION99.8485422189
6.6394-48.6840.2296481391071460.1980780311052580X-RAY DIFFRACTION99.2716678806

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