← Back to search
7ouh

Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor bictegravir

Method: ELECTRON MICROSCOPY Dmax: 154.7 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Integrase

Simian T-lymphotropic virus 1

UniProt Q4QY51

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 6 DNA 4 PDB declaration: decameric（10） Consistent with all polymer counts Chain A； UniProt 600–896 Chain B； UniProt 600–896 Chain D； UniProt 600–896 Chain E； UniProt 600–896 Mutation：A219E PC4 and SFRS1-interacting protein,Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform × 2 ;DNA (5'-D(*AP*CP*TP*GP*TP*GP*TP*TP*TP*GP*GP*CP*GP*CP*TP*TP*CP*TP*CP*TP*C)-3') ; × 2 ;DNA (5'-D(*GP*AP*GP*AP*GP*AP*AP*GP*CP*GP*CP*CP*AP*AP*AP*CP*AP*CP*A)-3') ; × 2 ZN ZINC ION × 4 MG MAGNESIUM ION × 4 KLQ Bictegravir × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.50 Å

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 7OUH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7OUF Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor XZ450 Deposited 2021-06-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: decameric
Chain A 597–896（300 aa）
Chain B 597–896（300 aa）
Chain D 597–896（300 aa）
Chain E 597–896（300 aa）
Mutation：A219E Mutation：A219E Mutation：A219E Mutation：A219E ZN ZINC ION × 4 MG MAGNESIUM ION × 4 1L0 4-azanyl-~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-6-[3-(dimethylamino)-3-oxidanylidene-propyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7OUG STLV-1 intasome:B56 in complex with the strand-transfer inhibitor raltegravir Deposited 2021-06-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: decameric
Chain A 597–896（300 aa）
Chain B 597–896（300 aa）
Chain D 597–896（300 aa）
Chain E 597–896（300 aa）
Mutation：A219E Mutation：A219E Mutation：A219E Mutation：A219E ZN ZINC ION × 4 MG MAGNESIUM ION × 4 RLT N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7PEL CryoEM structure of simian T-cell lymphotropic virus intasome in complex with PP2A regulatory subunit B56 gamma Deposited 2021-08-10 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: decameric
Chain A 600–896（297 aa）
Chain B 600–896（297 aa）
Chain D 600–896（297 aa）
Chain E 600–896（297 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q4QY51_9STL1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–301； UniProt 600–896 Author chain B； PDBConstruct 5–301； UniProt 600–896 Author chain D； PDBConstruct 5–301； UniProt 600–896 Author chain E； PDBConstruct 5–301； UniProt 600–896

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 7ouh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ouh
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id7ouh
Deposition date deposition_date2021-06-11
Structure title titleStructure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor bictegravir
Keywords keywordsintegrase, intasome, HTLV, STLV, integration, strand-transfer inhibitors, INSTI, bictegravir, BIC, drug, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier44.31 Å
Radius of gyration Rg (electron density) rg_electron45.73 Å
Forward intensity I(0) i0759591000.00
Molecular weight molecular_weight215020.0 kDa
Excluded volume excluded_volume263700 ų
Envelope volume envelope_volume387480 ų
Hydration-shell volume shell_volume71246 ų
Envelope diameter envelope_diameter160.9 Å
Shell Rg shell_rg49.33 Å
Envelope Rg envelope_rg45.36 Å
Shape Rg shape_rg45.77 Å
Total Rg total_rg45.75 Å
Total atoms total_atoms15082
Residues n_residues1744
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
▼

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

Maximum dimension Dmax dmax154.7 Å
Rg (real space) rg_real44.53 Å
Rg uncertainty (real space) rg_real_error1.53 Å
I(0) (real space) i0_real7.5960e+08
I(0) uncertainty (real space) i0_real_error1.4170e+07
Rg (reciprocal space) rg_reciprocal44.32 Å
I(0) (reciprocal space) i0_reciprocal759400000.0000
Solution quality estimate total_estimate0.8443
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.3 Å
Skewness Skewness skewness0.520
Kurtosis Kurtosis kurtosis-0.221
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha93790000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.711; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.873
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (8)

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7ouhA01
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_id7ouhB01
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_id7ouhD01
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_id7ouhE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
▶

8. Citations (1)

▶

9. Files and Curves (10)