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2b4j

Structural basis for the recognition between HIV-1 integrase and LEDGF/p75

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

Integrase (IN)

Human immunodeficiency virus 1

UniProt P12497

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 PC4 and SFRS1 interacting protein × 2 （O75475） PHOSPHATE ION × 2 GLYCEROL × 4 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 8 PC4 and SFRS1 interacting protein × 4 （O75475） PHOSPHATE ION × 4 GLYCEROL × 8 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1b92 1b9d 1b9f 2gol 2gon 2gon 2gon 2gon 2h3f 2h3i 2h3q 2h3v

39 assemblies; showing the first 12

Homodimer
1a43 1a8o 1aum 1b92 1b9d 1b9f 1baj 1bhl 1bis 1biu 1biu 1itg

67 assemblies; showing the first 12

Homotetramer
4ipy 8a1p 8a1q 8buv 8cbr 8cbs 8cbt 8cbu 8cbv 8t5b 8v9c

11 assemblies

Other homooligomers
1bi4 1bl3 3h47 3h4e 3h4e 3mge 4qnb 8f22 8f22 8vc0 8vc0 8vxv

22 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
1afv 1ak4 1ak4 2b4j 2b4j 2xv6 2xv6 2xxm 3av9 3ava 3avb 3avc

73 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name POL_HV1N5
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–166； UniProt 765–927 Author chain B； PDBConstruct 4–166； UniProt 765–927

PC4 and SFRS1 interacting protein

Homo sapiens

UniProt O75475

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Integrase (IN) × 2 （P12497） PHOSPHATE ION × 2 GLYCEROL × 4 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 8 Integrase (IN) × 4 （P12497） PHOSPHATE ION × 4 GLYCEROL × 8 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1z9e 2m16 3zeh 4fu6 6zv0

5 assemblies

Homodimer
6trj 6tvm

2 assemblies

Homotetramer

None

Other homooligomers
5oym

1 assemblies

Heteromeric or nucleic-acid complex
2b4j 2b4j 2msr 2mtn 2n3a 3f9k 3f9k 3f9k 3f9k 3f9k 3f9k 3f9k

47 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PSIP1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 3–98； UniProt 347–442 Author chain D； PDBConstruct 3–98； UniProt 347–442

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_id2b4j
Deposition date deposition_date2005-09-24
Structure title titleStructural basis for the recognition between HIV-1 integrase and LEDGF/p75
Keywords keywordsHIV, integration, transcription, viral protein, recombination; viral protein, recombination
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.

2b4j__assembly_1__model_1

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

Download this curve (.dat)

2b4j__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2b4j__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）27.37 Å
Rg (electron density)26.84 Å
Total Rg27.66 Å
Atom count3537
Residues444
Excluded volume63482 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2b4j__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2b4j__assembly_2__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 (5)

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2b4ja_
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_idd2b4jb_
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_idd2b4jc1
Class classa — All alpha proteins
Fold Fold folda.48 — N-cbl like
Superfamily Superfamily superfamilya.48.4 — HIV integrase-binding domain
Family Family familya.48.4.1 — HIV integrase-binding domain
Domain ID domain_idd2b4jc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2b4jd2
Class classa — All alpha proteins
Fold Fold folda.48 — N-cbl like
Superfamily Superfamily superfamilya.48.4 — HIV integrase-binding domain
Family Family familya.48.4.1 — HIV integrase-binding domain
Domain ID domain_idd2b4jd3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id2b4jA00
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_id2b4jB00
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_id2b4jC00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily10 — Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
Domain ID domain_id2b4jD00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily10 — Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
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7. Citations (1)