3OYB: Prototype Foamy Virus (PFV) intasome

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI MK2048. Determined by X-ray diffraction at 2.54 Å resolution. Released 17 Nov 2010.

Method
X-ray diffraction
Resolution
2.54 Å
Organism
Human spumaretrovirus
Chains
4
Atoms
5,398
Mol. weight
101.12 kDa
Ligands
ZZX, MG, ZN
Released
17 Nov 2010

Explore 3OYB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3OYB contains 38 α-helices and 29 β-strands across 2 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: 27 helices, 22 β-strands

ElementResiduesLengthSheet
α-helix9-168
β-strand30-3341
β-strand36-4161
β-strand44-4741
α-helix51-6313
α-helix69-779
β-strand8011
α-helix85-939
α-helix97-1026
α-helix104-1052
β-strand108-10922
α-helix110-1134
α-helix115-1184
β-strand124-13073
α-helix132-1332
α-helix1351
β-strand13614
β-strand13914
β-strand141-14773
β-strand153-15863
α-helix163-17412
β-strand181-18443
α-helix188-1914
α-helix193-2008
α-helix2041
β-strand205-20843
α-helix209-2102
α-helix214-2174
α-helix218-23518
α-helix243-2453
α-helix246-2549
β-strand25815
β-strand26315
α-helix265-2706
α-helix288-30013
α-helix308-3114
β-strand314-31522
β-strand322-32546
β-strand32617
α-helix3271
α-helix330-3312
β-strand33717
α-helix338-3403
β-strand341-34886
β-strand351-35556
β-strand361-36556
α-helix366-3683
β-strand369-37136
α-helix3721
Chain B: 11 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix117-1193
β-strand124-13078
β-strand13619
β-strand13919
β-strand141-14778
β-strand153-15868
α-helix163-17311
β-strand181-18448
α-helix188-1914
α-helix193-2019
α-helix2041
β-strand205-20848
α-helix209-2102
α-helix218-23518
α-helix242-25413
α-helix265-2706
α-helix286-2872
α-helix288-2925

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
PFV integraseA, Bprotein395Human spumaretrovirusP14350
DNA (5'-d(*ap*tp*tp*gp*tp*cp*ap*tp*gp*gp*ap*ap*tp*tp*tp*cp*gp*cp*a)-3')CDNA19
DNA (5'-d(*tp*gp*cp*gp*ap*ap*ap*tp*tp*cp*cp*ap*tp*gp*ap*cp*a)-3')DDNA17
Sequence of entity 1 (A, B), FASTA
>3OYB_1 PFV integrase (chains A, B)
GPGCNTKKPNLDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKI
VLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNKASGPILRPDR
PQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIA
IPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVG
RPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQE
IRTSLYHPSTPPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDH
LGNNRTVSIDNLKPTSHQNGTTNDTATMDHLEKNE
Sequence of entity 2 (C), FASTA
>3OYB_2 DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3') (chains C)
ATTGTCATGGAATTTCGCA
Sequence of entity 3 (D), FASTA
>3OYB_3 DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3') (chains D)
TGCGAAATTCCATGACA

Ligands and cofactors

IDNameFormulaCopies
ZZX(6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,…C21 H21 Cl F N5 O41
MGMagnesium ionMg3
ZNZinc ionZn1

Water and common crystallization additives (NH4, GOL, SO4) are not listed.

Primary citation

Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance. Hare, S., Vos, A.M., Clayton, R.F. et al. Proc Natl Acad Sci U S A (2010) 107:20057-20062. DOI 10.1073/pnas.1010246107 · PubMed

Other PDB entries of the same protein (UniProt P14350), best resolution first:

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