6VOY: HTLV-1 instasome

Cryo-EM structure of HTLV-1 instasome. Determined by electron microscopy at 3.7 Å resolution. Released 1 Jul 2020.

Method
Electron microscopy
Resolution
3.7 Å
Organisms
Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2), Human T-cell leukemia virus type I, Homo sapiens
Chains
12
Atoms
17,556
Mol. weight
313.41 kDa
Ligands
ZN, MG
Released
1 Jul 2020

Explore 6VOY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VOY contains 96 α-helices and 33 β-strands across 6 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: 13 helices, 8 β-strands

ElementResiduesLengthSheet
α-helix6-94
α-helix13-197
α-helix25-295
α-helix34-396
β-strand62-6541
β-strand75-8061
β-strand87-9261
α-helix97-10711
α-helix123-1264
α-helix128-1358
α-helix149-1524
α-helix153-17119
α-helix180-19011
α-helix202-2076
α-helix208-2114
β-strand228-23032
β-strand24913
β-strand254-25853
β-strand262-26653
α-helix268-2703
β-strand271-27332
Chain B: 12 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix2-98
α-helix17-193
α-helix23-308
β-strand62-6544
β-strand76-8054
β-strand87-9044
α-helix97-10913
α-helix123-1264
α-helix128-1347
α-helix135-1373
α-helix149-1513
α-helix152-17019
α-helix180-18910
α-helix202-2065
α-helix209-2157
β-strand228-23035
β-strand241-24445
β-strand25816
β-strand26216
Chain C: 15 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix3-97
α-helix13-197
α-helix23-297
α-helix34-385
α-helix46-472
β-strand61-6667
β-strand75-8067
β-strand87-9267
α-helix97-10711
β-strand11918
α-helix123-1264
α-helix128-1358
β-strand14318
α-helix144-1452
α-helix149-1524
α-helix153-17119
α-helix178-19114
α-helix202-2076
α-helix208-2114
β-strand25319
β-strand258110
β-strand262110
β-strand26719
α-helix268-2703
Chain D: 12 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix2-98
α-helix17-193
α-helix23-319
β-strand62-65411
β-strand75-80611
β-strand87-92611
α-helix97-10913
β-strand116-117212
α-helix123-1253
α-helix128-1347
α-helix135-1373
β-strand140-141212
α-helix149-1513
α-helix152-17019
α-helix180-18910
α-helix202-2054
α-helix208-2158
β-strand230113
β-strand241113
β-strand258114
β-strand262114
Chains E and F: 22 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix39-479
α-helix64-8219
α-helix89-913
α-helix92-10312
α-helix131-14515
α-helix152-1554
α-helix161-1688
α-helix169-1724
α-helix176-19217
α-helix195-21218
α-helix222-23312
α-helix242-2465
α-helix247-2515
α-helix253-2564
α-helix260-2623
α-helix264-27512
α-helix278-2858
α-helix288-2914
α-helix299-30911
α-helix321-33111
α-helix342-3454
α-helix354-3596

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA-binding protein 7dA, B, C, Dprotein390Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2), Human T-cell leukemia virus type IP14078, P39476 (AlphaFold model)
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoformE, Fprotein343Homo sapiensQ13362 (AlphaFold model)
DNA (5'-d(p*ap*cp*ap*cp*ap*cp*tp*tp*gp*ap*cp*tp*ap*gp*gp*gp*tp*g)-3')I, LDNA49Homo sapiens
DNA (25-mer)J, MDNA25Human T-cell leukemia virus type I
DNA (5'-d(p*ap*cp*ap*cp*ap*cp*tp*tp*gp*ap*cp*tp*ap*gp*gp*gp*tp*g)-3')K, NDNA20Human T-cell leukemia virus type I
Sequence of entity 1 (A, B, C, D), FASTA
>6VOY_1 DNA-binding protein 7d (chains A, B, C, D)
MGSSHHHHHHSSGLVPRGSHMATVKFKYKGEEKEVDISKIKKVARVGKMISFTYDEGGGK
TGEGAVSEKDAPKELLQMLEKQKKGGSLEVLFQGPSPAELHSFTHCGQTALTLQGATTTE
ASNILRSCHACRKNNPQHQMPRGHIRRGLLPNHIWQGDITHFKYKNTLYRLHVWVDTFSG
AISATQKRKETSSEAISSLLQAIAYLGKPSYINTDNGPAYISQDFLNMCTSLAIRHTTHV
PYNPTSSGLVQRSNGILKTLLYKYFTDKPDLPMDNALSIALWTINHLNVLTNCHKTRWQL
HHSPRLQPIPETRSLSNKQTHWYYFKLPGLNSRQWKGPQEALQEAAGAALIPVSASSAQW
IPWRLLKRAACPRPVGGPADPKEKDHQHHG
Sequence of entity 2 (E, F), FASTA
>6VOY_2 Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform (chains E, F)
IRDVPPADQEKLFIQKLRQCCVLFDFVSDPLSDLKWKEVKRAALSEMVEYITHNRNVITE
PIYPEVVHMFAVNMFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQLVYEFFLRFLESPD
FQPNIAKKYIDQKFVLQLLELFDSEDPRERDFLKTTLHRIYGKFLGLRAYIRKQINNIFY
RFIYETEHHNGIAELLEILGSIINGFALPLKEEHKIFLLKVLLPLHKVKSLSVYHPQLAY
CVVQFLEKDSTLTEPVVMALLKYWPKTHSPKEVMFLNELEEILDVIEPSEFVKIMEPLFR
QLAKCVSSPHFQVAERALYYWNNEYIMSLISDNAAKILPIMFP
Sequence of entity 3 (I, L), FASTA
>6VOY_3 DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3') (chains I, L)
CCAGGAGAGAAATTTAGTACACAGATATCCACCCTAGTCAAGTGTGTCC
Sequence of entity 4 (J, M), FASTA
>6VOY_4 DNA (25-MER) (chains J, M)
ACTGTGTACTAAATTTCTCTCCTGG
Sequence of entity 5 (K, N), FASTA
>6VOY_5 DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3') (chains K, N)
GGACACACTTGACTAGGGTG

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn4
MGMagnesium ionMg2

Primary citation

Structural basis of host protein hijacking in human T-cell leukemia virus integration. Bhatt, V., Shi, K., Salamango, D.J. et al. Nat Commun (2020) 11:3121-3121. DOI 10.1038/s41467-020-16963-6 · PubMed

Other PDB entries of the same protein (UniProt P14078), best resolution first:

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