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7jn3

Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

integrase

Rous sarcoma virus (strain Schmidt-Ruppin A)

UniProt P03354

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 8 DNA 4 ;DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*T)-3') ; × 2 ;DNA (5'-D(*AP*TP*TP*GP*CP*AP*TP*AP*AP*GP*AP*CP*AP*AP*CP*A)-3') ; × 2 ZINC ION × 2 ;(6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide ; × 2 MAGNESIUM ION × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
5kz9 5kza 5kzb 6ccj 6ce5 6cus 6cv8 6cw4

8 assemblies

Homodimer
1a5v 1a5v 1a5w 1a5x 1asu 1asv 1asw 1c0m 1c0m 1c1a 1cxq 1cxu

26 assemblies; showing the first 12

Homotetramer
5kz9 5kzb

2 assemblies

Other homooligomers
3tir

1 assemblies

Heteromeric or nucleic-acid complex
5ejk 7jn3 7ku7 7kui 8e14

5 assemblies

View Construct and Data Evidence
UniProt name POL_RSVP
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–278； UniProt 1281–1558 Author chain B； PDBConstruct 1–278； UniProt 1281–1558 Author chain C； PDBConstruct 1–278； UniProt 1281–1558 Author chain D； PDBConstruct 1–278； UniProt 1281–1558 Author chain E； PDBConstruct 1–278； UniProt 1281–1558 Author chain F； PDBConstruct 1–278； UniProt 1281–1558 Author chain G； PDBConstruct 1–278； UniProt 1281–1558 Author chain H； PDBConstruct 1–278； UniProt 1281–1558

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id7jn3
Deposition date deposition_date2020-08-03
Structure title titleCryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048
Keywords keywordsintasome, integrase-viral DNA complex, HYDROLASE-DNA-INHIBITOR complex; HYDROLASE/DNA/INHIBITOR
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7jn3__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7jn3__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

7jn3__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）49.61 Å
Rg (electron density)50.90 Å
Total Rg50.81 Å
Atom count15666
Residues1875
Excluded volume274460 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7jn3__assembly_1__model_1 dodecameric （12） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7jn3A01
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_id7jn3A02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily10 — Integrase, C-terminal domain superfamily, retroviral
Domain ID domain_id7jn3E01
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_id7jn3E02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily10 — Integrase, C-terminal domain superfamily, retroviral
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7. Citations (1)