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6bsi

Structure of HIV-1 RT complexed with an RNA/DNA hybrid containing the polypurine-tract sequence

Method: X-RAY DIFFRACTION Dmax: 107.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

REVERSE TRANSCRIPTASE P66 SUBUNIT

Human immunodeficiency virus 1

UniProt Q74085

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 DNA 1 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain A； UniProt 168–724 Not recorded REVERSE TRANSCRIPTASE P51 SUBUNIT × 1 （A0A076Q3N8） ;DNA (5'-D(*GP*TP*TP*TP*TP*TP*CP*TP*TP*TP*TP*GP*TP*TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3') ; × 1 RNA (25-MER) × 1 EFZ (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；Sodium citrate pH 5.2, CaCl2, PEG400 Resolution 3.25 Å R-free 0.241

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6BSI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6BSG Structure of HIV-1 RT complexed with RNA/DNA hybrid in an RNA hydrolysis-off mode Deposited 2017-12-03 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 168–724（557 aa）
Not recorded EFZ (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 4 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Sodium citrate pH 5.2, CaCl2, PEG400
Resolution 2.44 Å R-free 0.224
6BSJ Structure of HIV-1 RT complexed with an RNA/DNA hybrid sequence non-preferred for RNA hydrolysis Deposited 2017-12-03 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 168–724（557 aa）
Not recorded EFZ (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 4 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Sodium citrate pH 5.2, CaCl2, PEG400
Resolution 2.89 Å R-free 0.251

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q74085_9HIV1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–558； UniProt 168–724

REVERSE TRANSCRIPTASE P51 SUBUNIT

Human immunodeficiency virus 1

UniProt A0A076Q3N8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 DNA 1 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain B； UniProt 168–607 Not recorded REVERSE TRANSCRIPTASE P66 SUBUNIT × 1 （Q74085） ;DNA (5'-D(*GP*TP*TP*TP*TP*TP*CP*TP*TP*TP*TP*GP*TP*TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3') ; × 1 RNA (25-MER) × 1 EFZ (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；Sodium citrate pH 5.2, CaCl2, PEG400 Resolution 3.25 Å R-free 0.241

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6BSI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6BHJ Structure of HIV-1 Reverse Transcriptase Bound to a 38-mer Hairpin Template-Primer RNA-DNA Aptamer Deposited 2017-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 166–722（557 aa）
Chain B 168–595（428 aa）
Mutation：C280S, D498N Mutation：C280S MG MAGNESIUM ION × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；278 K；10% PEG 8000, 25 mM BisTris-Propane pH 6.8, 75 mM BisTris-Propane pH 7.4, 50 mM Ammonium Sulfate, 5% glycerol, 5% sucrose
Resolution 2.81 Å R-free 0.244
6BHJ Structure of HIV-1 Reverse Transcriptase Bound to a 38-mer Hairpin Template-Primer RNA-DNA Aptamer Deposited 2017-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain C 166–722（557 aa）
Chain D 168–595（428 aa）
Mutation：C280S, D498N Mutation：C280S MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；278 K；10% PEG 8000, 25 mM BisTris-Propane pH 6.8, 75 mM BisTris-Propane pH 7.4, 50 mM Ammonium Sulfate, 5% glycerol, 5% sucrose
Resolution 2.81 Å R-free 0.244
6BSG Structure of HIV-1 RT complexed with RNA/DNA hybrid in an RNA hydrolysis-off mode Deposited 2017-12-03 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 168–607（440 aa）
Not recorded EFZ (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 4 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Sodium citrate pH 5.2, CaCl2, PEG400
Resolution 2.44 Å R-free 0.224
6BSH Structure of HIV-1 RT complexed with RNA/DNA hybrid in the RNA hydrolysis mode Deposited 2017-12-03 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 168–607（440 aa）
Not recorded EFZ (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 6 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Sodium citrate pH 5.2, CaCl2, PEG400
Resolution 2.65 Å R-free 0.227
6BSJ Structure of HIV-1 RT complexed with an RNA/DNA hybrid sequence non-preferred for RNA hydrolysis Deposited 2017-12-03 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 168–607（440 aa）
Not recorded EFZ (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 4 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Sodium citrate pH 5.2, CaCl2, PEG400
Resolution 2.89 Å R-free 0.251
6VUG Diabody bound to a Reverse Transcriptase Aptamer Complex Deposited 2020-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain B 168–595（428 aa） Fragment：P51 subunit, residues 168-595
Not recorded SO4 SULFATE ION × 11 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.4 M Ammonium Sulfate 0.1 M HEPES pH 7.8 0.1 M NaCl
Resolution 3.00 Å R-free 0.255

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A076Q3N8_9HIV1
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–441； UniProt 168–607

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6bsi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6bsi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6bsi
Deposition date deposition_date2017-12-03
Structure title titleStructure of HIV-1 RT complexed with an RNA/DNA hybrid containing the polypurine-tract sequence
Keywords keywordsHIV-RT, DNA-RNA complex, RNase H, VIRAL PROTEIN, viral protein-dna-rna complex, viral protein-dna-rna-inhibitor complex; viral protein/dna/rna/inhibitor
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.61 Å
Radius of gyration Rg (electron density) rg_electron33.46 Å
Forward intensity I(0) i0248121000.00
Molecular weight molecular_weight121800.0 kDa
Excluded volume excluded_volume150160 ų
Envelope volume envelope_volume200100 ų
Hydration-shell volume shell_volume49399 ų
Envelope diameter envelope_diameter115.4 Å
Shell Rg shell_rg40.63 Å
Envelope Rg envelope_rg33.17 Å
Shape Rg shape_rg33.46 Å
Total Rg total_rg34.00 Å
Total atoms total_atoms8555
Residues n_residues996
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax107.4 Å
Rg (real space) rg_real33.55 Å
Rg uncertainty (real space) rg_real_error0.86 Å
I(0) (real space) i0_real2.4810e+08
I(0) uncertainty (real space) i0_real_error4.5110e+06
Rg (reciprocal space) rg_reciprocal33.59 Å
I(0) (reciprocal space) i0_reciprocal248100000.0000
Solution quality estimate total_estimate0.6781
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.9 Å
Skewness Skewness skewness0.298
Kurtosis Kurtosis kurtosis-0.350
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38360000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 0.078; Positv: 1.000; Valcen: 1.000; Smooth: 0.846
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id6bsiA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology10 — HIV Type 1 Reverse Transcriptase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — HIV Type 1 Reverse Transcriptase, subunit A, domain 1
Domain ID domain_id6bsiA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id6bsiA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id6bsiA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id6bsiA05
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id6bsiB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology10 — HIV Type 1 Reverse Transcriptase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — HIV Type 1 Reverse Transcriptase, subunit A, domain 1
Domain ID domain_id6bsiB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id6bsiB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id6bsiB04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
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8. Citations (1)

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9. Files and Curves (10)