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3l2u

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and GS9137 (Elvitegravir)

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Integrase

Human spumaretrovirus

UniProt P14350

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 4 DNA 4 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*TP*GP*TP*A)-3' × 2 5'-D(*TP*AP*CP*AP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3' × 2 ZINC ION × 2 MAGNESIUM ION × 6 AMMONIUM ION × 2 6-(3-chloro-2-fluorobenzyl)-1-[(1S)-1-(hydroxymethyl)-2-methylpropyl]-7-methoxy-4-oxo-1,4-dihydroquinoline-3-carboxylic acid × 2 GLYCEROL × 8 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2lsn

1 assemblies

Homodimer
2x6n 2x6n 2x6n 2x6s 2x6s 2x6s 2x74 2x74 2x74 2x78 2x78 3dlr

12 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3l2q 3l2r 3l2u 3l2v 3l2w 3os0 3os1 3os2 3oy9 3oya 3oyb 3oyc

51 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name POL_FOAMV
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–395； UniProt 752–1143 Author chain B； PDBConstruct 4–395； UniProt 752–1143

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_id3l2u
Deposition date deposition_date2009-12-15
Structure title titleCrystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and GS9137 (Elvitegravir)
Keywords keywords;PROTEIN-DNA COMPLEX, TETRAMER, DNA INTEGRATION, ENDONUCLEASE, METAL-BINDING, MULTIFUNCTIONAL ENZYME, NUCLEASE, NUCLEOTIDYLTRANSFERASE, NUCLEUS, TRANSFERASE, VIRAL NUCLEOPROTEIN, VIRION, ZINC, DNA-BINDING, ZINC BINDING, HHCC MOTIF, VIRAL PROTEIN, RECOMBINATION, RECOMBINATION-DNA complex ;; RECOMBINATION/DNA
Experimental Method methodX-RAY DIFFRACTION
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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.

3l2u__assembly_1__model_1

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

Download this curve (.dat)

3l2u__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.

3l2u__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）38.07 Å
Rg (electron density)38.84 Å
Total Rg38.91 Å
Atom count9888
Residues1128
Excluded volume172760 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3l2u__assembly_1__model_1 octameric （8） 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 (8)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3l2ua1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.10 — Retroviral integrase, N-terminal Zn binding domain
Family Family familya.4.10.0 — automated matches
Domain ID domain_idd3l2ua2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.2 — Retroviral integrase, catalytic domain
Domain ID domain_idd3l2ua3
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.7 — DNA-binding domain of retroviral integrase
Family Family familyb.34.7.1 — DNA-binding domain of retroviral integrase

CATH v4.4 (5 domains)

Domain ID domain_id3l2uA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily70 —
Domain ID domain_id3l2uA02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily140 —
Domain ID domain_id3l2uA03
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_id3l2uA04
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology20 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily110 —
Domain ID domain_id3l2uB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
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7. Citations (1)