4E7I: Pro-Pol polyprotein

PFV intasome freeze-trapped prior to 3'-processing, Mn-bound form (UI-Mn). Determined by X-ray diffraction at 2.53 Å resolution. Released 23 May 2012.

Method
X-ray diffraction
Resolution
2.53 Å
Organisms
Human spumaretrovirus, synthetic DNA
Chains
4
Atoms
5,483
Mol. weight
102.32 kDa
Ligands
HEZ, MN, ZN
Released
23 May 2012

Explore 4E7I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4E7I contains 40 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: 28 helices, 22 β-strands

ElementResiduesLengthSheet
α-helix9-168
β-strand30-3341
β-strand36-4161
β-strand44-4741
α-helix51-6515
α-helix69-768
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-helix163-17311
β-strand181-18443
α-helix188-1914
α-helix193-2008
α-helix2041
β-strand205-20843
α-helix209-2102
α-helix214-2174
α-helix218-23417
α-helix243-2453
α-helix246-2549
α-helix256-2572
β-strand25815
β-strand26315
α-helix265-2706
α-helix288-30013
α-helix307-3115
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: 12 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-helix257-2582
α-helix265-2706
α-helix286-2872
α-helix288-29710

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Pro-Pol polyproteinA, 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')CDNA19synthetic DNA
DNA (5'-d(*tp*gp*cp*gp*ap*ap*ap*tp*tp*cp*cp*ap*tp*gp*ap*cp*ap*ap*t)-3')DDNA19synthetic DNA
Sequence of entity 1 (A, B), FASTA
>4E7I_1 Pro-Pol polyprotein (chains A, B)
GPGCNTKKPNLDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKI
VLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNKASGPILRPDR
PQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIA
IPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVG
RPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQE
IRTSLYHPSTPPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDH
LGNNRTVSIDNLKPTSHQNGTTNDTATMDHLEKNE
Sequence of entity 2 (C), FASTA
>4E7I_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
>4E7I_3 DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*AP*AP*T)-3') (chains D)
TGCGAAATTCCATGACAAT

Ligands and cofactors

IDNameFormulaCopies
HEZHexane-1,6-diolC6 H14 O21
MNManganese (II) ionMn3
ZNZinc ionZn1

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

Primary citation

3'-Processing and strand transfer catalysed by retroviral integrase in crystallo. Hare, S., Maertens, G.N., Cherepanov, P. EMBO J (2012) 31:3020-3028. DOI 10.1038/emboj.2012.118 · PubMed

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

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