Integrase
Maedi visna virus
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.
| Other PDB | Difference from Current Entry 3HPH | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 3HPG Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces Deposited 2009-06-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 8 PDB declaration: octameric |
Chain A
823–1039(217 aa)
Fragment:N-terminal and catalytic core domains, UNP residues 823-1039
Chain B
823–1039(217 aa)
Fragment:N-terminal and catalytic core domains, UNP residues 823-1039
Chain E
823–1039(217 aa)
Fragment:N-terminal and catalytic core domains, UNP residues 823-1039
Chain F
823–1039(217 aa)
Fragment:N-terminal and catalytic core domains, UNP residues 823-1039
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.6;291 K;25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 3.28 Å R-free 0.253 |
| 3HPG Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces Deposited 2009-06-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 8 PDB declaration: octameric |
Chain C
823–1039(217 aa)
Fragment:N-terminal and catalytic core domains, UNP residues 823-1039
Chain D
823–1039(217 aa)
Fragment:N-terminal and catalytic core domains, UNP residues 823-1039
Chain E
823–1039(217 aa)
Fragment:N-terminal and catalytic core domains, UNP residues 823-1039
Chain F
823–1039(217 aa)
Fragment:N-terminal and catalytic core domains, UNP residues 823-1039
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.6;291 K;25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 3.28 Å R-free 0.253 |
| 3HPG Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces Deposited 2009-06-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer;Protein × 8 PDB declaration: octameric |
Chain A
823–1039(217 aa)
Fragment:N-terminal and catalytic core domains, UNP residues 823-1039
Chain B
823–1039(217 aa)
Fragment:N-terminal and catalytic core domains, UNP residues 823-1039
Chain C
823–1039(217 aa)
Fragment:N-terminal and catalytic core domains, UNP residues 823-1039
Chain D
823–1039(217 aa)
Fragment:N-terminal and catalytic core domains, UNP residues 823-1039
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.6;291 K;25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 3.28 Å R-free 0.253 |
| 5LLJ Maedi-Visna virus (MVV) integrase C-terminal domain (residues 220-276) Deposited 2016-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain A
1039–1096(58 aa)
Chain B
1039–1096(58 aa)
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;0.2M potassium sodium tartrate 0.1M BTP pH 7.5 20% PEG-3350
|
Resolution 1.78 Å R-free 0.234 |
| 5M0R Cryo-EM reconstruction of the maedi-visna virus (MVV) strand transfer complex Deposited 2016-10-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer;Protein × 16 PDB declaration: 22-meric |
Chain A
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain B
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain C
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain D
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain E
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain F
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain G
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain H
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain I
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain J
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain K
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain L
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain M
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain N
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain O
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain P
821–1101(281 aa)
Fragment:UNP residues 821-1101
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE;To lower salt concentration before plunge-freezing, the grids were blotted for 0.5 s, immediately hydrated with a 4-ul drop of 200 mM NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl pH 6.5 and blotted again for 2.5 s followed by plunging into liquid ethane.
|
Resolution 8.20 Å |
| 5T3A Maedi-Visna virus (MVV) integrase CCD-CTD (residues 60-275) Deposited 2016-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain A
880–1101(222 aa)
|
Not recorded | ACT ACETATE ION × 6 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6;291 K;0.1M Mes pH6.0, 15-100mM calcium acetate and 15-21% PEG 400
|
Resolution 2.50 Å R-free 0.240 |
| 7U32 MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution Deposited 2022-02-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer;Protein × 16 PDB declaration: eicosameric |
Chain A
1226–1506(281 aa)
Chain B
1226–1506(281 aa)
Chain C
1226–1506(281 aa)
Chain D
1226–1506(281 aa)
Chain E
1226–1506(281 aa)
Chain F
1226–1506(281 aa)
Chain G
1226–1506(281 aa)
Chain H
1226–1506(281 aa)
Chain I
1226–1506(281 aa)
Chain J
1226–1506(281 aa)
Chain K
1226–1506(281 aa)
Chain L
1226–1506(281 aa)
Chain M
1226–1506(281 aa)
Chain N
1226–1506(281 aa)
Chain O
1226–1506(281 aa)
Chain P
1226–1506(281 aa)
|
Not recorded | ZN ZINC ION × 12 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE;Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C
|
Resolution 3.46 Å |
| 7Z1Z MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution Deposited 2022-02-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer;Protein × 18 PDB declaration: 24-meric |
Chain A
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain B
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain C
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain D
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain E
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain F
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain G
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain H
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain I
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain J
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain K
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain L
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain M
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain N
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain O
821–1101(281 aa)
Fragment:UNP residues 821-1101
Chain P
821–1101(281 aa)
Fragment:UNP residues 821-1101
|
Not recorded | ZN ZINC ION × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5;310 mM NaCl, 3 mM CaCl2, 25 mM BisTris-HCl, pH 6.5.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7ZPP Cryo-EM structure of the MVV CSC intasome at 4.5A resolution Deposited 2022-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer;Protein × 16 PDB declaration: eicosameric |
Chain A
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain B
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain C
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain D
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain E
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain F
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain G
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain H
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain I
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain J
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain K
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain L
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain M
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain N
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain O
1226–1506(281 aa)
Fragment:UNP residues 821-1101
Chain P
1226–1506(281 aa)
Fragment:UNP residues 821-1101
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5;1 M NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl, pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE;To lower salt concentration before plunge-freezing, the grids were blotted for 0.5 s, immediately hydrated with a 4-ul drop of 200 mM NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl pH 6.5 and blotted again for 2.5 s followed by plunging into liquid ethane.
|
Resolution 4.50 Å |
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 |