3HPH: Closed tetramer of Visna virus integrase
Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD. Determined by X-ray diffraction at 2.64 Å resolution. Released 28 Jul 2009.
- Method
- X-ray diffraction
- Resolution
- 2.64 Å
- Organisms
- Maedi visna virus, Homo sapiens
- Chains
- 8
- Atoms
- 8,778
- Mol. weight
- 145.23 kDa
- Ligands
- ZN, PO4
- Released
- 28 Jul 2009
Explore 3HPH in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3HPH contains 77 α-helices and 24 β-strands across 8 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, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 19-25 | 7 | |
| α-helix | 30-37 | 8 | |
| β-strand | 62-70 | 9 | 1 |
| β-strand | 73-80 | 8 | 1 |
| β-strand | 86-91 | 6 | 1 |
| α-helix | 96-110 | 15 | |
| β-strand | 114-117 | 4 | 1 |
| α-helix | 121-124 | 4 | |
| α-helix | 126-135 | 10 | |
| β-strand | 138-141 | 4 | 1 |
| α-helix | 143-145 | 3 | |
| α-helix | 147-167 | 21 | |
| α-helix | 168-170 | 3 | |
| α-helix | 174-183 | 10 | |
| α-helix | 184-188 | 5 | |
| α-helix | 197-212 | 16 | |
Chain B: 11 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 19-26 | 8 | |
| α-helix | 30-38 | 9 | |
| β-strand | 62-70 | 9 | 2 |
| β-strand | 73-80 | 8 | 2 |
| β-strand | 86-91 | 6 | 2 |
| α-helix | 96-110 | 15 | |
| β-strand | 114-117 | 4 | 2 |
| α-helix | 121-124 | 4 | |
| α-helix | 126-135 | 10 | |
| β-strand | 138-141 | 4 | 2 |
| α-helix | 152-167 | 16 | |
| α-helix | 168-170 | 3 | |
| α-helix | 174-183 | 10 | |
| α-helix | 184-188 | 5 | |
| β-strand | 191 | 1 | 3 |
| β-strand | 195 | 1 | 3 |
| α-helix | 197-212 | 16 | |
Chain C: 11 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 19-26 | 8 | |
| α-helix | 30-38 | 9 | |
| β-strand | 62-70 | 9 | 4 |
| β-strand | 73-80 | 8 | 4 |
| β-strand | 86-91 | 6 | 4 |
| α-helix | 96-110 | 15 | |
| β-strand | 114-118 | 5 | 4 |
| α-helix | 121-124 | 4 | |
| α-helix | 126-135 | 10 | |
| β-strand | 138-142 | 5 | 4 |
| α-helix | 152-167 | 16 | |
| α-helix | 168-170 | 3 | |
| α-helix | 174-183 | 10 | |
| α-helix | 184-188 | 5 | |
| β-strand | 191 | 1 | 5 |
| β-strand | 195 | 1 | 5 |
| α-helix | 197-212 | 16 | |
Chain D: 12 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 19-25 | 7 | |
| α-helix | 30-37 | 8 | |
| β-strand | 62-70 | 9 | 6 |
| β-strand | 73-80 | 8 | 6 |
| β-strand | 86-91 | 6 | 6 |
| α-helix | 96-110 | 15 | |
| β-strand | 114-117 | 4 | 6 |
| α-helix | 121-124 | 4 | |
| α-helix | 126-134 | 9 | |
| β-strand | 138-141 | 4 | 6 |
| α-helix | 143-145 | 3 | |
| α-helix | 147-167 | 21 | |
| α-helix | 168-170 | 3 | |
| α-helix | 174-183 | 10 | |
| α-helix | 184-188 | 5 | |
| α-helix | 197-213 | 17 | |
Chains E and H: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 349-362 | 14 | |
| α-helix | 365-367 | 3 | |
| α-helix | 370-382 | 13 | |
| α-helix | 387-390 | 4 | |
| α-helix | 391-393 | 3 | |
| α-helix | 394-402 | 9 | |
| α-helix | 403-405 | 3 | |
| α-helix | 410-427 | 18 | |
| α-helix | 435-439 | 5 | |
Chain F: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 353-362 | 10 | |
| α-helix | 365-367 | 3 | |
| α-helix | 370-377 | 8 | |
| α-helix | 397-402 | 6 | |
| α-helix | 403-405 | 3 | |
| α-helix | 410-423 | 14 | |
Chain G: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 354-362 | 9 | |
| α-helix | 365-367 | 3 | |
| α-helix | 370-377 | 8 | |
| α-helix | 378-380 | 3 | |
| α-helix | 397-402 | 6 | |
| α-helix | 403-405 | 3 | |
| α-helix | 410-419 | 10 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Integrase | A, B, C, D | protein | 219 | Maedi visna virus | P35956 |
| PC4 and SFRS1-interacting protein | E, F, G, H | protein | 94 | Homo sapiens | O75475 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D), FASTA
>3HPH_1 Integrase (chains A, B, C, D)
MVENIPLAEEEHNKWHQDAVSLHLEFGIPRTAAEDIVQQCDVCQENKMPSTLRGSNKRGI
DHWQVDYTHYEDKIILVWVETNSGLIYAERVKGETGQEFRVQTMKWYAMFAPKSLQSDNG
PAFVAESTQLLMKYLGIEHTTGIPWNPQSQALVERTHQTLKNTLEKLIPMFNAFESALAG
TLITLNIKRKGGLGTSPMDIFIFNKEQQRIQQQSKSKQE
Sequence of entity 2 (E, F, G, H), FASTA
>3HPH_2 PC4 and SFRS1-interacting protein (chains E, F, G, H)
MDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFK
VSQVIMEKSTMLYNKFKNMFLVGEGDSVLEVLFQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
| PO4 | Phosphate ion | O4 P | 3 |
Water and common crystallization additives (GOL) are not listed.
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)
- 9S28 2.8 Å, MVV STC intasome in complex with LEDGF
- 9S29 2.8 Å, MVV CSC intasome in complex with LEDGF
- 3HPG 3.28 Å, Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open…
- 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
Browse structure collections
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