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

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Basic information

Entry
Database: PDB / ID: 6oun
TitleStructure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and (-)3TC-TP
Components
  • DNA primer 20-mer
  • DNA template 27-mer
  • P51 RT
  • Reverse transcriptase/ribonuclease H
KeywordsTRANSFERASE/DNA / Reverse Transcriptase / ternary complex / (-)3TC-TP / chain terminator / lamivudine / stereochemistry / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / 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 / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion 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. / 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
Lamivudine 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: 2.656 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 4, 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)132,73310
Polymers131,9274
Non-polymers8066
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14010 Å2
ΔGint-97 kcal/mol
Surface area44220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.011, 171.784, 105.885
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 / Exoribonuclease 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 BH10)
Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P03366, 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 BH10)
Strain: isolate BH10 / Gene: gag-pol / Variant: isolate BH10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03366

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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, 17 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.89 Å3/Da / Density % sol: 57.43 % / Description: plates
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 3-6% (w/v) PEG 8000, 15 mM magnesium sulfate, and 50 mM MES adjusted at pH 6.0
PH range: 5.5-6.0

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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: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.656→30 Å / Num. obs: 44155 / % possible obs: 99.8 % / Redundancy: 26.3 % / CC1/2: 0.999 / Rsym value: 0.13 / Net I/σ(I): 19.54
Reflection shellResolution: 2.656→2.82 Å / Redundancy: 28.6 % / Mean I/σ(I) obs: 1.93 / Num. unique obs: 6977 / CC1/2: 0.92 / Rsym value: 1.48 / % possible all: 99.5

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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: 3KJV

3kjv


Resolution: 2.656→29.571 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 2205 5 %
Rwork0.207 --
obs0.2096 44086 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.656→29.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7350 824 44 11 8229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058514
X-RAY DIFFRACTIONf_angle_d0.76311812
X-RAY DIFFRACTIONf_dihedral_angle_d15.3144868
X-RAY DIFFRACTIONf_chiral_restr0.0471321
X-RAY DIFFRACTIONf_plane_restr0.0051353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6562-2.7140.37871350.3052567X-RAY DIFFRACTION99
2.714-2.7770.37381340.3042548X-RAY DIFFRACTION99
2.777-2.84640.3651360.30292588X-RAY DIFFRACTION100
2.8464-2.92330.39481370.29822592X-RAY DIFFRACTION100
2.9233-3.00930.33571370.28142600X-RAY DIFFRACTION100
3.0093-3.10630.35311360.27542582X-RAY DIFFRACTION100
3.1063-3.21720.28491370.24512602X-RAY DIFFRACTION100
3.2172-3.34580.26191370.23352597X-RAY DIFFRACTION100
3.3458-3.49790.30091370.22922600X-RAY DIFFRACTION100
3.4979-3.6820.26871380.21312625X-RAY DIFFRACTION100
3.682-3.91220.26071380.20142621X-RAY DIFFRACTION100
3.9122-4.21350.19881380.17472626X-RAY DIFFRACTION100
4.2135-4.6360.24511390.16712639X-RAY DIFFRACTION100
4.636-5.30350.20091400.1752651X-RAY DIFFRACTION100
5.3035-6.66920.27251410.21212677X-RAY DIFFRACTION100
6.6692-29.5730.24141450.19312766X-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)
17.38060.06930.54165.84410.22485.3614-0.26750.26450.07050.2426-0.44311.85290.6333-0.12550.5910.6303-0.01150.04210.5936-0.04450.899718.226537.8836-37.9968
27.3534-3.70132.28912.1237-1.56469.62810.49391.7011-0.05670.0014-0.74430.94860.24430.38990.25551.0040.0316-0.01060.777-0.08650.93537.014317.2161-36.8216
32.16110.9474-2.4889.86115.9998.48680.84150.71460.1487-1.7447-0.7683-0.8384-0.3285-1.17880.11220.9791-0.0471-0.1190.7810.04770.785535.07767.207-32.9212
46.3421-5.29653.6756.7224-3.03192.1104-0.18580.4829-0.30510.75180.10141.06990.0623-0.06580.13920.97120.04430.03150.81230.07890.878220.716235.7029-37.5765
51.5547-0.11190.15623.2653-0.08151.98750.04350.1538-0.3855-0.266-0.0015-0.00620.5891-0.0838-0.0490.8497-0.00190.01470.5504-0.03950.590341.56312.1353-22.8274
60.7712-0.25070.36424.5502-0.28481.6854-0.01560.39850.249-0.7868-0.1161-0.30780.16370.15790.12880.6508-0.0080.11280.63740.03660.529147.148731.2906-34.044
71.7536-1.01761.51232.9115-1.11242.6566-0.104300.4278-0.2043-0.1217-0.6829-0.1920.23560.22230.5892-0.02620.1480.54410.03650.642437.749252.1981-28.8885
83.8482-0.23630.18975.353-0.85832.3936-0.04060.36780.312-0.7662-0.0466-0.0014-0.04480.08030.06480.7817-0.01420.05270.53530.10420.62724.878559.805-43.6751
91.7098-1.9061-1.55112.94841.69421.654-0.046-0.1796-0.26810.2343-0.04780.15560.1825-0.17010.13820.67970.0050.01210.62790.05480.531623.076423.0341-3.6467
105.7232-0.73591.50257.76771.36917.98250.0296-1.2461-0.3720.3578-0.09770.0331-0.4371-0.1263-0.10420.7825-0.06970.09911.0529-0.00280.674615.495939.242311.7315
111.4470.5495-0.75673.7213-2.51431.86420.1615-0.2410.24860.54120.14190.3834-0.455-0.2846-0.32280.69230.00480.06360.6647-0.03020.709112.734661.3784-19.0172
127.3736-0.3205-0.55565.1173-1.65812.894-0.06040.14210.2416-0.12430.0172-0.3699-0.0220.16170.02770.54630.0251-0.00290.5536-0.08460.497422.687244.9416-14.0886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'P' and (resid 805 through 814 )
2X-RAY DIFFRACTION2chain 'P' and (resid 815 through 821 )
3X-RAY DIFFRACTION3chain 'T' and (resid 704 through 708 )
4X-RAY DIFFRACTION4chain 'T' and (resid 709 through 725 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1 through 253 )
6X-RAY DIFFRACTION6chain 'A' and (resid 254 through 382 )
7X-RAY DIFFRACTION7chain 'A' and (resid 383 through 451 )
8X-RAY DIFFRACTION8chain 'A' and (resid 452 through 555 )
9X-RAY DIFFRACTION9chain 'B' and (resid 6 through 174 )
10X-RAY DIFFRACTION10chain 'B' and (resid 175 through 208 )
11X-RAY DIFFRACTION11chain 'B' and (resid 209 through 335 )
12X-RAY DIFFRACTION12chain 'B' and (resid 336 through 430 )

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