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- PDB-6p1i: Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsD... -

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Basic information

Entry
Database: PDB / ID: 6p1i
TitleStructure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and dCTP
Components
  • DNA Primer 20-mer
  • DNA template 27-mer
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE/DNA / Reverse Transcriptase / ternary complex / chain terminator / stereochemistry / TRANSFERASE / TRANSFERASE-DNA complex / dCTP
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 / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / 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: 2.74 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 19, 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

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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)132,8479
Polymers132,1394
Non-polymers7085
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14870 Å2
ΔGint-96 kcal/mol
Surface area44810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.417, 169.504, 103.063
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


Mass: 64521.895 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(DE3) (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(DE3) (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 , 4 types, 21 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
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: 2.74→30 Å / Num. obs: 38484 / % possible obs: 99.1 % / Redundancy: 13.5 % / Biso Wilson estimate: 56.79 Å2 / CC1/2: 1 / Rsym value: 0.16 / Net I/σ(I): 12.4
Reflection shellResolution: 2.74→2.9 Å / Mean I/σ(I) obs: 2.28 / Num. unique obs: 5873 / CC1/2: 0.865 / Rsym value: 0.9

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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: 2.74→28.927 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.77
RfactorNum. reflection% reflection
Rfree0.2365 1925 5 %
Rwork0.1828 --
obs0.1855 38466 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.74→28.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7510 845 40 16 8411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078696
X-RAY DIFFRACTIONf_angle_d0.90412026
X-RAY DIFFRACTIONf_dihedral_angle_d17.8225040
X-RAY DIFFRACTIONf_chiral_restr0.051334
X-RAY DIFFRACTIONf_plane_restr0.0061377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7359-2.80430.4791220.38882318X-RAY DIFFRACTION89
2.8043-2.88010.35481370.26592597X-RAY DIFFRACTION100
2.8801-2.96470.29141380.24352624X-RAY DIFFRACTION100
2.9647-3.06030.29191350.23112563X-RAY DIFFRACTION100
3.0603-3.16960.30581370.22572593X-RAY DIFFRACTION100
3.1696-3.29630.27641380.21322628X-RAY DIFFRACTION100
3.2963-3.44610.26651380.20372610X-RAY DIFFRACTION100
3.4461-3.62750.25751370.1852614X-RAY DIFFRACTION100
3.6275-3.85420.22571380.16722623X-RAY DIFFRACTION100
3.8542-4.1510.21051390.14952634X-RAY DIFFRACTION100
4.151-4.56730.18791390.13982634X-RAY DIFFRACTION100
4.5673-5.22480.19881390.14732654X-RAY DIFFRACTION100
5.2248-6.570.24471410.18352680X-RAY DIFFRACTION100
6.57-28.92830.19171470.17682769X-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)
11.9221-0.02340.0532.887-0.17362.1843-0.06350.313-0.542-0.539-0.00280.45250.6161-0.28210.02270.5837-0.0518-0.09830.4422-0.07210.54431.5033-9.6522-28.6137
24.4784-1.1697-0.62382.9007-0.48113.0512-0.61670.72320.127-0.76360.1998-0.1176-0.0977-0.14860.14380.69-0.1213-0.10620.4853-0.08630.350839.2957-2.2635-33.747
31.3360.10930.39731.8159-0.37780.77170.0431-0.01350.0523-0.086-0.01180.21720.037-0.1517-0.04080.3164-0.02430.00040.3237-0.02180.322438.34345.6207-19.2019
41.5842-0.32420.60442.0675-0.68480.40440.05410.4679-0.2468-0.3466-0.3955-0.16770.2622-0.0120.31840.6357-0.0328-0.1910.4862-0.04960.575129.8617-12.999-32.6903
50.60650.00960.00862.7366-0.74610.64730.01670.0813-0.0899-0.3901-0.0327-0.30690.20810.1029-0.00640.33020.02440.03360.308-0.03160.283548.6469.0238-21.2509
60.9239-0.2892-0.01463.1265-0.69650.2265-0.01220.28980.1123-0.503-0.0682-0.3710.01870.14360.02640.33260.00720.06880.39850.04760.368847.241931.7965-31.1244
71.0144-1.11380.68171.8428-0.72871.3156-0.1875-0.18270.20560.28-0.0212-0.387-0.1833-0.0130.17840.3411-0.05980.06060.340.01260.458137.449852.9247-28.4399
81.7406-0.6680.47032.38940.08522.67550.12880.22070.04410.0086-0.1666-0.04530.096-0.00070.02580.2861-0.03770.0730.30840.04390.303524.285157.6599-43.8398
93.1471.7334-0.3372.64590.97934.4748-0.45120.2131-0.22260.1987-0.16971.18680.0927-0.1159-0.31390.4771-0.06790.18240.63220.04890.80598.66815.0662-8.5529
102.6831-0.73610.70983.03690.39821.2443-0.02960.0980.13010.39450.14540.26270.06880.1474-0.0910.34270.05360.03790.41460.02480.311629.080521.3371-6.2727
116.32246.3842-3.28359.3916-7.77098.4452-0.63480.3761-0.34890.0530.4438-0.04570.08-1.34910.27910.53720.0281-0.01230.65830.21930.584912.520721.0831-13.7356
122.0298-0.4155-0.14780.84470.75260.98960.1347-0.148-0.42430.2313-0.15630.2295-0.2654-0.42750.09190.48160.06660.12310.48630.14870.293521.714722.375-2.3285
132.25070.22970.23321.89160.62271.97340.0189-0.49870.28880.2497-0.0977-0.0348-0.53180.06480.12140.71140.02780.20050.63160.00590.530612.636834.764310.6971
143.0432-0.21690.23843.9767-1.50333.82570.5218-0.75850.2865-0.01240.00920.1464-1.03530.6603-0.50390.8688-0.05850.120.824-0.02350.398617.670840.9399.4998
151.14340.6187-0.84752.519-0.80141.45130.1698-0.15580.25560.22110.05750.492-0.1492-0.2068-0.19870.3112-0.00920.09570.49550.02470.512910.478864.9595-23.2632
164.37690.0718-0.12862.87470.2221.5304-0.12280.21780.15960.15160.2721-0.115-0.02940.0142-0.13130.34720.03010.05790.3782-0.00820.334722.042544.4735-13.7788
171.8910.5411-0.05160.2935-0.35230.8243-0.73691.560.00930.15630.31191.20950.4462-1.1071-0.12070.3967-0.07740.18550.6869-0.12961.15029.189240.1435-42.1345
180.871-0.70820.17974.5977-2.58691.7123-0.6566-0.6660.28180.39590.9810.1239-0.5277-0.1995-0.38530.53520.1968-0.02790.65990.00560.674723.09637.8527-35.679
195.3077-0.2181-1.00665.60590.08063.170.0650.1951-0.96091.4846-0.675-0.28820.98830.27490.41850.97070.17510.06640.6250.07040.933826.696322.1449-33.4768
201.375-0.35410.5991.5502-0.92830.67080.31980.3067-0.2482-0.251-0.00320.393-0.3322-0.4341-0.24120.64680.18280.08340.54630.01130.3443.252114.3498-33.9921
215.09931.32062.62078.92492.68843.3755-0.33551.13610.4021-2.0133-0.0785-0.8424-0.00030.05580.35210.84360.0062-0.02530.54050.04740.521235.32764.7501-33.6626
220.8973-0.03670.3652.249-0.27081.59530.08580.21470.3126-0.4844-0.66820.36850.19780.12810.47540.65420.0361-0.08230.33670.0090.357337.80219.3424-28.4225
232.269-1.38640.69983.81340.71250.85010.19790.7301-0.18820.403-0.43180.9351-0.0004-0.11910.27460.83590.18490.06670.61860.1180.661321.477532.2715-36.5007
248.9077-1.57411.69211.9877-2.21783.5527-1.82761.0381-0.0650.15930.8257-0.7319-1.4327-0.20.79770.5980.0328-0.14990.74140.10890.85875.737649.8416-42.7889
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 83:84 )B83 - 84
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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