3hph

Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD

Method: X-RAY DIFFRACTION Dmax: 149.5 Å Quality: REASONABLE

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

Integrase

Maedi visna virus

UniProt P35956

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 823–1039 Chain B; UniProt 823–1039 Chain C; UniProt 823–1039 Chain D; UniProt 823–1039 Fragment:N-terminal and catalytic domains, UNP residues 923-1039 PC4 and SFRS1-interacting protein × 4 (O75475) ZN ZINC ION × 4 GOL GLYCEROL × 4 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;0.7-0.9M (NH4)2HPO4, 2.5% Jeffamine M600,100mM Bis-Tris propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.64 Å R-free 0.253

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.

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POL_VILVK
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–219; UniProt 823–1039 Author chain B; PDBConstruct 3–219; UniProt 823–1039 Author chain C; PDBConstruct 3–219; UniProt 823–1039 Author chain D; PDBConstruct 3–219; UniProt 823–1039

PC4 and SFRS1-interacting protein

Homo sapiens

UniProt O75475

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain E; UniProt 348–435 Chain F; UniProt 348–435 Chain G; UniProt 348–435 Chain H; UniProt 348–435 Fragment:Integrase binding domain, UNP residues 348-435 Integrase × 4 (P35956) ZN ZINC ION × 4 GOL GLYCEROL × 4 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;0.7-0.9M (NH4)2HPO4, 2.5% Jeffamine M600,100mM Bis-Tris propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.64 Å R-free 0.253

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.

34 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PSIP1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain E; PDBConstruct 1–88; UniProt 348–435 Author chain F; PDBConstruct 1–88; UniProt 348–435 Author chain G; PDBConstruct 1–88; UniProt 348–435 Author chain H; PDBConstruct 1–88; UniProt 348–435

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 3hph

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3hph
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3hph
Deposition date deposition_date2009-06-04
Structure title titleClosed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD
Keywords keywords;PROTEIN-PROTEIN COMPLEX, TETRAMER, DNA INTEGRATION, ENDONUCLEASE, MAGNESIUM, METAL-BINDING, MULTIFUNCTIONAL ENZYME, NUCLEASE, NUCLEOTIDYLTRANSFERASE, NUCLEUS, TRANSFERASE, VIRAL NUCLEOPROTEIN, VIRION, DNA-BINDING, HOST-VIRUS INTERACTION, TRANSCRIPTION, TRANSCRIPTION REGULATION, ZINC BINDING, HHCC MOTIF, VIRAL PROTEIN, RECOMBINATION ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.01
Radius of gyration Rg (electron density) rg_electron37.03
Forward intensity I(0) i0234249000.00
Molecular weight molecular_weight123550.0 kDa
Excluded volume excluded_volume154680 ų
Envelope volume envelope_volume207100 ų
Hydration-shell volume shell_volume48111 ų
Envelope diameter envelope_diameter160.6
Shell Rg shell_rg41.33
Envelope Rg envelope_rg38.08
Shape Rg shape_rg36.96
Total Rg total_rg37.54
Total atoms total_atoms8668
Residues n_residues1086
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 dmax149.5
Rg (real space) rg_real37.24
Rg uncertainty (real space) rg_real_error2.29
I(0) (real space) i0_real2.3420e+08
I(0) uncertainty (real space) i0_real_error5.1630e+06
Rg (reciprocal space) rg_reciprocal37.09
I(0) (reciprocal space) i0_reciprocal234200000.0000
Solution quality estimate total_estimate0.6885
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.2
Skewness Skewness skewness0.569
Kurtosis Kurtosis kurtosis0.179
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha48560000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.472; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.531; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3hphe1
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_idd3hphe2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3hphf_
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_idd3hphg_
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_idd3hphh1
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_idd3hphh2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (11 domains)

Domain ID domain_id3hphA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily200 — Integrase, N-terminal zinc-binding domain
Domain ID domain_id3hphA02
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_id3hphB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily200 — Integrase, N-terminal zinc-binding domain
Domain ID domain_id3hphB02
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_id3hphC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily200 — Integrase, N-terminal zinc-binding domain
Domain ID domain_id3hphC02
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_id3hphD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily200 — Integrase, N-terminal zinc-binding domain
Domain ID domain_id3hphD02
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_id3hphE00
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_id3hphF00
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_id3hphH00
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

8. Citations (2)

9. Files and Curves (10)