3HPG: Visna virus integrase
Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces. Determined by X-ray diffraction at 3.28 Å resolution. Released 28 Jul 2009.
- Method
- X-ray diffraction
- Resolution
- 3.28 Å
- Organisms
- Maedi visna virus, Homo sapiens
- Chains
- 12
- Atoms
- 12,792
- Mol. weight
- 217.39 kDa
- Ligands
- ZN
- Released
- 28 Jul 2009
Explore 3HPG in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3HPG contains 101 α-helices and 42 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 12 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 19-26 | 8 | |
| α-helix | 30-38 | 9 | |
| α-helix | 41-44 | 4 | |
| β-strand | 62-69 | 8 | 1 |
| β-strand | 74-80 | 7 | 1 |
| β-strand | 86-91 | 6 | 1 |
| α-helix | 96-109 | 14 | |
| β-strand | 114-116 | 3 | 1 |
| α-helix | 121-124 | 4 | |
| α-helix | 126-135 | 10 | |
| β-strand | 138-140 | 3 | 1 |
| α-helix | 149-167 | 19 | |
| α-helix | 168-170 | 3 | |
| α-helix | 174-183 | 10 | |
| α-helix | 184-188 | 5 | |
| β-strand | 191 | 1 | 2 |
| β-strand | 195 | 1 | 2 |
| α-helix | 197-210 | 14 | |
Chain B: 12 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 19-26 | 8 | |
| α-helix | 30-38 | 9 | |
| α-helix | 41-45 | 5 | |
| β-strand | 62-69 | 8 | 3 |
| β-strand | 74-80 | 7 | 3 |
| β-strand | 86-91 | 6 | 3 |
| α-helix | 96-109 | 14 | |
| β-strand | 114-117 | 4 | 3 |
| α-helix | 121-124 | 4 | |
| α-helix | 126-135 | 10 | |
| β-strand | 138-141 | 4 | 3 |
| α-helix | 149-167 | 19 | |
| α-helix | 168-170 | 3 | |
| α-helix | 174-183 | 10 | |
| α-helix | 184-188 | 5 | |
| β-strand | 191 | 1 | 4 |
| β-strand | 195 | 1 | 4 |
| α-helix | 197-210 | 14 | |
Chains C and F: 12 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 19-26 | 8 | |
| α-helix | 30-38 | 9 | |
| α-helix | 41-44 | 4 | |
| β-strand | 62-69 | 8 | 5 |
| β-strand | 74-80 | 7 | 5 |
| β-strand | 86-91 | 6 | 5 |
| α-helix | 96-109 | 14 | |
| β-strand | 114-117 | 4 | 5 |
| α-helix | 121-124 | 4 | |
| α-helix | 126-135 | 10 | |
| β-strand | 138-141 | 4 | 5 |
| α-helix | 149-167 | 19 | |
| α-helix | 168-170 | 3 | |
| α-helix | 174-183 | 10 | |
| α-helix | 184-188 | 5 | |
| β-strand | 191 | 1 | 6 |
| β-strand | 195 | 1 | 6 |
| α-helix | 197-210 | 14 | |
Chain D: 12 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 19-26 | 8 | |
| α-helix | 30-38 | 9 | |
| α-helix | 41-45 | 5 | |
| β-strand | 62-69 | 8 | 7 |
| β-strand | 74-80 | 7 | 7 |
| β-strand | 86-91 | 6 | 7 |
| α-helix | 96-109 | 14 | |
| β-strand | 114-116 | 3 | 7 |
| α-helix | 121-124 | 4 | |
| α-helix | 126-135 | 10 | |
| β-strand | 138-140 | 3 | 7 |
| α-helix | 149-167 | 19 | |
| α-helix | 168-170 | 3 | |
| α-helix | 174-183 | 10 | |
| α-helix | 184-188 | 5 | |
| β-strand | 191 | 1 | 8 |
| β-strand | 195 | 1 | 8 |
| α-helix | 197-210 | 14 | |
Chain E: 12 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 19-26 | 8 | |
| α-helix | 30-38 | 9 | |
| α-helix | 41-45 | 5 | |
| β-strand | 62-69 | 8 | 9 |
| β-strand | 74-80 | 7 | 9 |
| β-strand | 86-91 | 6 | 9 |
| α-helix | 96-109 | 14 | |
| β-strand | 114-116 | 3 | 9 |
| α-helix | 121-124 | 4 | |
| α-helix | 126-135 | 10 | |
| β-strand | 138-140 | 3 | 9 |
| α-helix | 152-167 | 16 | |
| α-helix | 168-170 | 3 | |
| α-helix | 174-183 | 10 | |
| α-helix | 184-188 | 5 | |
| β-strand | 191 | 1 | 10 |
| β-strand | 195 | 1 | 10 |
| α-helix | 197-210 | 14 | |
Chain G: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 349-361 | 13 | |
| α-helix | 365-367 | 3 | |
| α-helix | 370-378 | 9 | |
| α-helix | 395-402 | 8 | |
| α-helix | 410-422 | 13 | |
Chain H: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 348-361 | 14 | |
| α-helix | 365-367 | 3 | |
| α-helix | 370-378 | 9 | |
| α-helix | 395-402 | 8 | |
| α-helix | 410-417 | 8 | |
Chain I: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 349-361 | 13 | |
| α-helix | 365-367 | 3 | |
| α-helix | 370-378 | 9 | |
| α-helix | 395-402 | 8 | |
| α-helix | 410-417 | 8 | |
3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Integrase | A, B, C, D, E, F | protein | 219 | Maedi visna virus | P35956 |
| PC4 and SFRS1-interacting protein | G, H, I, J, K, L | protein | 95 | Homo sapiens | O75475 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>3HPG_1 Integrase (chains A, B, C, D, E, F)
MVENIPLAEEEHNKWHQDAVSLHLEFGIPRTAAEDIVQQCDVCQENKMPSTLRGSNKRGI
DHWQVDYTHYEDKIILVWVETNSGLIYAERVKGETGQEFRVQTMKWYAMFAPKSLQSDNG
PAFVAESTQLLMKYLGIEHTTGIPWNPQSQALVERTHQTLKNTLEKLIPMFNAFESALAG
TLITLNIKRKGGLGTSPMDIFIFNKEQQRIQQQSKSKQE
Sequence of entity 2 (G, H, I, J, K, L), FASTA
>3HPG_2 PC4 and SFRS1-interacting protein (chains G, H, I, J, K, L)
SMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRF
KVSQVIMEKSTMLYNKFKNMFLVGEGDSVLEVLFQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 6 |
Primary citation
Structural basis for functional tetramerization of lentiviral integrase. Hare, S., Di Nunzio, F., Labeja, A. et al. PLoS Pathog (2009) 5:e1000515-e1000515. DOI 10.1371/journal.ppat.1000515 · PubMed
Other PDB entries of the same protein (UniProt P35956), best resolution first:
- 5LLJ 1.78 Å, Maedi-Visna virus (MVV) integrase C-terminal domain (residues 220-276)
- 5T3A 2.5 Å, Maedi-Visna virus (MVV) integrase CCD-CTD (residues 60-275)
- 3HPH 2.64 Å, Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD
- 9S28 2.8 Å, MVV STC intasome in complex with LEDGF
- 9S29 2.8 Å, MVV CSC intasome in complex with LEDGF
- 7U32 3.46 Å, MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution
- 7Z1Z 3.5 Å, MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution
- 7ZPP 4.5 Å, Cryo-EM structure of the MVV CSC intasome at 4.5A resolution
- 5M0R 8.2 Å, Cryo-EM reconstruction of the maedi-visna virus (MVV) strand transfer complex
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