6bsj

Structure of HIV-1 RT complexed with an RNA/DNA hybrid sequence non-preferred for RNA hydrolysis

Method: X-RAY DIFFRACTION Dmax: 108.6 Å Quality: REASONABLE

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*AP*TP*GP*CP*CP*TP*AP*TP*AP*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 × 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

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.

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*AP*TP*GP*CP*CP*TP*AP*TP*AP*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 × 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

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.

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 6bsj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6bsj
Deposition date deposition_date2017-12-03
Structure title titleStructure of HIV-1 RT complexed with an RNA/DNA hybrid sequence non-preferred for RNA hydrolysis
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

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.70
Radius of gyration Rg (electron density) rg_electron33.59
Forward intensity I(0) i0256282000.00
Molecular weight molecular_weight123730.0 kDa
Excluded volume excluded_volume152620 ų
Envelope volume envelope_volume202620 ų
Hydration-shell volume shell_volume49955 ų
Envelope diameter envelope_diameter116.4
Shell Rg shell_rg40.58
Envelope Rg envelope_rg33.30
Shape Rg shape_rg33.58
Total Rg total_rg34.16
Total atoms total_atoms8687
Residues n_residues990
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax108.6
Rg (real space) rg_real33.64
Rg uncertainty (real space) rg_real_error0.76
I(0) (real space) i0_real2.5630e+08
I(0) uncertainty (real space) i0_real_error4.4560e+06
Rg (reciprocal space) rg_reciprocal33.68
I(0) (reciprocal space) i0_reciprocal256300000.0000
Solution quality estimate total_estimate0.6772
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.3
Skewness Skewness skewness0.303
Kurtosis Kurtosis kurtosis-0.339
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38730000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 0.078; Positv: 1.000; Valcen: 1.000; Smooth: 0.869

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id6bsjA01
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_id6bsjA02
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_id6bsjA03
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_id6bsjA04
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_id6bsjA05
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_id6bsjB01
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_id6bsjB02
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_id6bsjB03
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_id6bsjB04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain

8. Citations (1)

9. Files and Curves (10)