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- PDB-6ujx: HIV-1 wild-type reverse transcriptase-DNA complex with (-)-FTC-TP -

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Basic information

Entry
Database: PDB / ID: 6ujx
TitleHIV-1 wild-type reverse transcriptase-DNA complex with (-)-FTC-TP
Components
  • DNA primer
  • DNA template
  • 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 / 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 / protein processing / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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
Chem-1RY / 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: 2.70451211695 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: DNA primer
T: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,97510
Polymers132,0794
Non-polymers8966
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-98 kcal/mol
Surface area46950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.804, 167.685, 103.309
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 / 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, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P04585, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#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, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P04585, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds

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DNA chain , 2 types, 2 molecules PT

#3: DNA chain DNA primer


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


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, 118 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-1RY / [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 487.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13FN3O12P3S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2% PEG 4000, 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: 2.65→50 Å / Num. obs: 39743 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 46.2408981058 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.8
Reflection shellResolution: 2.65→2.7 Å / Rmerge(I) obs: 0.735 / Num. unique obs: 3373

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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: 2.70451211695→47.5975379997 Å / SU ML: 0.3227080861 / Cross valid method: THROUGHOUT / σ(F): 1.33617033594 / Phase error: 27.3473199799
RfactorNum. reflection% reflection
Rfree0.24381306141 3502 5.04589138798 %
Rwork0.196688207566 --
obs0.199062841517 39631 89.1107287761 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.6637549949 Å2
Refinement stepCycle: LAST / Resolution: 2.70451211695→47.5975379997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7750 820 49 112 8731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009603591137988947
X-RAY DIFFRACTIONf_angle_d1.1519516652612326
X-RAY DIFFRACTIONf_chiral_restr0.04795625851261337
X-RAY DIFFRACTIONf_plane_restr0.00602033882581400
X-RAY DIFFRACTIONf_dihedral_angle_d19.40987255553426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.70451211695-2.74160.320866536353460.29111523714928X-RAY DIFFRACTION31.3687600644
2.7416-2.78070.325825961193970.2904354926381707X-RAY DIFFRACTION57.415658816
2.7807-2.82220.2723119126481010.2654941480691837X-RAY DIFFRACTION62.2550594282
2.8222-2.86630.2971191643631060.268876417661941X-RAY DIFFRACTION65.6510583708
2.8663-2.91330.3119047330031180.2573592401592202X-RAY DIFFRACTION74.3113388853
2.9133-2.96350.3196115891291330.2545459029222411X-RAY DIFFRACTION82.3834196891
2.9635-3.01740.3359723824081430.2666975517292585X-RAY DIFFRACTION88.256227758
3.0174-3.07540.3298612005871420.2526863737372757X-RAY DIFFRACTION92.3542529468
3.0754-3.13820.3056382320121610.2561423289692844X-RAY DIFFRACTION95.6701687361
3.1382-3.20640.2792974397871540.2239603414812865X-RAY DIFFRACTION97.5129198966
3.2064-3.2810.2882727839391540.232112667212889X-RAY DIFFRACTION98.3198707593
3.281-3.3630.2624684515561460.2171530697092928X-RAY DIFFRACTION98.0542264753
3.363-3.45390.2603630422871550.2210098901052889X-RAY DIFFRACTION98.0354267311
3.4539-3.55550.2957987137341540.2223439862712906X-RAY DIFFRACTION98.3922829582
3.5555-3.67020.2487881374031580.2214325261732911X-RAY DIFFRACTION98.0511182109
3.6702-3.80140.233511339851370.2063514537632921X-RAY DIFFRACTION98.6451612903
3.8014-3.95350.2688407727841530.1945381910092907X-RAY DIFFRACTION97.359210945
3.9535-4.13330.2323389368831530.1739718115872921X-RAY DIFFRACTION98.683788122
4.1333-4.35110.2011354358861600.1720074827452899X-RAY DIFFRACTION98.9327296248
4.3511-4.62350.2167887193221490.1573187836822912X-RAY DIFFRACTION98.5194721596
4.6235-4.98020.2039793967531640.1570131180432928X-RAY DIFFRACTION98.8807163415
4.9802-5.48070.2143896939461440.1534262781972960X-RAY DIFFRACTION99.8391765841
5.4807-6.27220.2062672055881580.1729118915232965X-RAY DIFFRACTION99.9040307102
6.2722-7.89650.2214701460141560.1742251896092968X-RAY DIFFRACTION99.968
7.8965-47.59753790.1985063248841600.1726820616722920X-RAY DIFFRACTION99.0353697749

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