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- PDB-6otz: Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsD... -

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Basic information

Entry
Database: PDB / ID: 6otz
TitleStructure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and (+)FTC-TP
Components
  • DNA Primer 20-mer
  • DNA template 27-mer
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE/DNA / Reverse Transcriptase / ternary complex / (-)FTC-TP / chain terminator / emtricitabine / stereochemistry / TRANSFERASE / TRANSFERASE-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 / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / 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-N8G / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.857 Å
AuthorsBertoletti, N. / Anderson, K.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049551 United States
CitationJournal: Protein Sci. / Year: 2019
Title: Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active ...Title: Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine.
Authors: Bertoletti, N. / Chan, A.H. / Schinazi, R.F. / Yin, Y.W. / Anderson, K.S.
History
DepositionMay 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
P: DNA Primer 20-mer
T: DNA template 27-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,84311
Polymers131,9274
Non-polymers9167
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-105 kcal/mol
Surface area45190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.069, 170.368, 103.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 64309.605 Da / Num. of mol.: 1 / Mutation: C280S, Q258C
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 BL21 (bacteria)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein p51 RT


Mass: 52748.418 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 (isolate HXB2)
Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P04585

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DNA chain , 2 types, 2 molecules PT

#3: DNA chain DNA Primer 20-mer


Mass: 6460.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA template 27-mer


Mass: 8408.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 21 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-N8G / [[(2~{S},5~{R})-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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.97 % / Description: plates
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 6-10% (w/v) PEG 8000, 15 mM magnesium sulfate, and 50 mM MES adjusted at pH 6.0
PH range: 5.5-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.857→30 Å / Num. obs: 34440 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.996 / Rpim(I) all: 0.075 / Rsym value: 0.16 / Net I/σ(I): 12.54
Reflection shellResolution: 2.857→3.03 Å / Num. unique obs: 5442 / CC1/2: 0.889 / Rpim(I) all: 0.43 / Rsym value: 0.854 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OR7

6or7


Resolution: 2.857→29.821 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 1720 5 %
Rwork0.1981 --
obs0.2002 34423 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.857→29.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7575 845 51 14 8485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038787
X-RAY DIFFRACTIONf_angle_d0.62512159
X-RAY DIFFRACTIONf_dihedral_angle_d16.3745069
X-RAY DIFFRACTIONf_chiral_restr0.0431342
X-RAY DIFFRACTIONf_plane_restr0.0051400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8569-2.94080.43751400.35652669X-RAY DIFFRACTION99
2.9408-3.03570.33641420.28322688X-RAY DIFFRACTION100
3.0357-3.14410.28591410.25722686X-RAY DIFFRACTION100
3.1441-3.26980.25051430.23412704X-RAY DIFFRACTION100
3.2698-3.41840.30521420.23262708X-RAY DIFFRACTION100
3.4184-3.59840.22941430.20482716X-RAY DIFFRACTION100
3.5984-3.82340.24531420.22700X-RAY DIFFRACTION100
3.8234-4.11790.25731440.18182725X-RAY DIFFRACTION100
4.1179-4.5310.19281430.16532719X-RAY DIFFRACTION100
4.531-5.18370.19081450.162753X-RAY DIFFRACTION100
5.1837-6.51960.22221450.1922764X-RAY DIFFRACTION100
6.5196-29.82280.23151500.18062871X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3656-0.5422-0.92553.9636-0.32252.1474-0.07710.4253-0.5431-0.659-0.01930.47540.5233-0.3184-0.00810.6184-0.0613-0.10780.4262-0.06230.531531.6802-9.6858-28.6922
22.4306-2.40110.25915.3082-0.10925.3084-0.2660.70260.153-0.61950.1812-0.238-0.26410.18140.28750.6856-0.1282-0.07240.3908-0.08580.401939.8597-2.2672-33.6006
31.69440.3780.08142.147-0.47051.2658-0.03990.1103-0.1225-0.26180.11620.18740.0516-0.0933-0.13440.3719-0.0238-0.00110.3328-0.01520.352238.66735.7197-19.1468
45.45081.6015-2.15471.0136-1.82493.67-0.94271.06390.4228-0.13020.21450.13071.267-0.52540.92810.7842-0.1046-0.1420.5024-0.01280.445531.288-16.1961-35.2768
50.4578-0.27180.12832.8007-0.68970.1996-0.03170.1109-0.0271-0.4254-0.0241-0.40470.16230.11180.03030.40090.0060.04380.3572-0.02980.335248.62679.0304-21.1698
60.6561-0.2863-0.09193.5561-0.5120.1619-0.07070.23430.1221-0.3972-0.0476-0.4835-0.06290.06320.06720.2915-0.04210.07560.39720.03530.418547.315732.0179-31.0484
71.601-0.60360.81981.9821-0.45822.2137-0.0081-0.23020.26260.229-0.075-0.3035-0.12560.00890.02730.3519-0.0570.05980.34830.02610.501337.48753.0793-28.5005
82.96130.33140.2873.5731-0.08852.85520.05730.31570.1607-0.1635-0.15320.0056-0.0451-0.29150.0720.253-0.0190.04640.33010.05680.316924.11558.0363-43.9096
92.09340.6869-0.14483.04140.89340.3182-0.1996-0.4464-0.620.2313-0.12350.82750.085-0.37080.03150.4475-0.02750.17770.75930.10521.1828.678215.1844-8.6115
102.3561-0.91550.23833.53921.11222.6046-0.11430.02090.17180.3530.12350.3665-0.01270.22680.08430.35170.0260.08370.38060.06690.328429.223121.7-6.3059
113.6384-2.0984-5.30814.54411.59598.5471-0.3868-0.31270.29530.1880.22020.1116-0.19810.15660.12620.54650.05390.0560.77470.17490.88158.847521.9335-10.0918
121.9323-0.8234-0.08711.61620.08540.65140.68380.1222-0.2340.5448-0.23440.1602-0.4464-0.63390.21060.56160.08380.23190.43640.09420.296921.853622.2055-2.4206
132.13810.16860.40172.26761.18344.4531-0.0463-0.8464-0.05390.7706-0.04950.5174-0.6927-0.11870.04040.77110.11330.31740.69870.02860.636412.484734.412110.5875
143.8664-0.2508-0.15393.4346-2.67646.07080.1998-1.20750.4810.35860.8496-0.1986-1.1933-0.3487-0.48321.1219-0.12660.1980.86820.01510.497618.310137.862210.2442
152.05041.3739-1.0934.1053-1.01011.25610.3638-0.40770.41980.3945-0.22340.8866-0.1682-0.0226-0.20130.37260.02140.13210.49850.00960.55310.359765.3332-23.3874
164.8487-0.89460.06564.158-0.54681.7707-0.05850.25670.3850.21960.1404-0.1172-0.1670.1088-0.1460.41050.03840.08050.3856-0.01380.41122.071744.6451-13.8603
171.43631.0833-2.6772.8221-1.30895.2185-1.04631.5622-0.08750.15810.66921.00480.7522-1.60390.06250.4559-0.0810.1950.6826-0.05331.23089.335940.492-42.1961
185.48571.2998-1.39178.7084-0.68142.0862-1.2138-0.3893-0.34260.45560.6744-0.13720.01520.02780.380.49450.12310.00210.60940.06350.707123.111438.0626-35.7969
198.58632.1030.19056.2981-3.09862.77180.3037-0.0741-1.72640.9164-0.7715-0.3820.86-0.44060.99971.24810.15570.16060.520.00550.883326.627522.2096-33.4444
205.25030.4271-2.11345.9995-0.13522.68420.31240.52040.3154-0.1351-0.3381-0.0225-0.5152-0.89020.04480.54550.12040.05620.534-0.00830.328743.341914.4368-33.9586
215.12785.8225.266.55375.99055.4689-0.14261.04970.4654-1.61270.7647-0.5455-0.26020.6732-0.42870.7623-0.0225-0.09150.50920.02290.528935.2624.708-33.5458
223.98350.3054-0.81040.6514-0.21544.88650.3170.42270.0967-0.7125-0.28680.72160.2864-0.8146-0.30160.66230.0592-0.03070.3335-0.00670.342437.83719.4387-28.3344
234.6646-2.83841.83069.1940.6761.4708-0.1540.6358-0.67750.7919-0.07741.6964-0.0058-0.25160.22920.85420.19420.08650.7320.06330.613421.550932.385-36.5614
241.7982-3.5111.89777.0257-3.82482.0645-1.02911.01631.21180.25141.263-0.2304-1.6957-1.10880.19130.74610.1974-0.04371.18120.3031.20115.745749.9327-42.6957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:62 )A1 - 62
2X-RAY DIFFRACTION2( CHAIN A AND RESID 63:79 )A63 - 79
3X-RAY DIFFRACTION3( CHAIN A AND RESID 80:125 )A80 - 125
4X-RAY DIFFRACTION4( CHAIN A AND RESID 126:142 )A126 - 142
5X-RAY DIFFRACTION5( CHAIN A AND RESID 143:277 )A143 - 277
6X-RAY DIFFRACTION6( CHAIN A AND RESID 278:387 )A278 - 387
7X-RAY DIFFRACTION7( CHAIN A AND RESID 388:448 )A388 - 448
8X-RAY DIFFRACTION8( CHAIN A AND RESID 449:554 )A449 - 554
9X-RAY DIFFRACTION9( CHAIN B AND RESID 6:16 )B6 - 16
10X-RAY DIFFRACTION10( CHAIN B AND RESID 17:82 )B17 - 82
11X-RAY DIFFRACTION11( CHAIN B AND RESID 83:87 )B83 - 87
12X-RAY DIFFRACTION12( CHAIN B AND RESID 96:153 )B96 - 153
13X-RAY DIFFRACTION13( CHAIN B AND RESID 154:204 )B154 - 204
14X-RAY DIFFRACTION14( CHAIN B AND RESID 205:240 )B205 - 240
15X-RAY DIFFRACTION15( CHAIN B AND RESID 241:324 )B241 - 324
16X-RAY DIFFRACTION16( CHAIN B AND RESID 325:429 )B325 - 429
17X-RAY DIFFRACTION17( CHAIN P AND RESID 805:808 )P805 - 808
18X-RAY DIFFRACTION18( CHAIN P AND RESID 809:812 )P809 - 812
19X-RAY DIFFRACTION19( CHAIN P AND RESID 813:816 )P813 - 816
20X-RAY DIFFRACTION20( CHAIN P AND RESID 818:821 )P818 - 821
21X-RAY DIFFRACTION21( CHAIN T AND RESID 704:707 )T704 - 707
22X-RAY DIFFRACTION22( CHAIN T AND RESID 708:711 )T708 - 711
23X-RAY DIFFRACTION23( CHAIN T AND RESID 712:721 )T712 - 721
24X-RAY DIFFRACTION24( CHAIN T AND RESID 722:725 )T722 - 725

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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