7OUH: STLV intasome:B56 complex

Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor bictegravir. Determined by electron microscopy at 3.5 Å resolution. Released 18 Aug 2021.

Method
Electron microscopy
Resolution
3.5 Å
Organisms
Simian T-lymphotropic virus 1, Homo sapiens
Chains
10
Atoms
15,088
Mol. weight
333.45 kDa
Ligands
ZN, MG, KLQ
Released
18 Aug 2021

Explore 7OUH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OUH contains 102 α-helices and 52 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.

Chains A and D: 13 helices, 13 β-strands

ElementResiduesLengthSheet
α-helix4-118
α-helix15-206
α-helix25-3410
β-strand61-70109
β-strand75-8399
β-strand89-9469
α-helix99-11214
β-strand118-12149
α-helix130-1389
β-strand142-14549
α-helix158-17417
α-helix182-1898
α-helix190-1945
β-strand196110
β-strand203110
α-helix204-2085
α-helix210-2156
α-helix223-2253
α-helix227-2282
β-strand229-232411
β-strand246-247211
β-strand251112
β-strand255-258412
β-strand266-269412
α-helix270-2723
β-strand273-275311
Chain B: 15 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix4-118
α-helix15-195
α-helix25-3410
α-helix37-404
β-strand61-711113
β-strand74-831013
β-strand89-94613
α-helix99-11214
β-strand118-121413
α-helix130-1389
β-strand142-145413
α-helix151-1544
α-helix155-17420
α-helix180-18910
α-helix190-1945
α-helix1951
β-strand196114
α-helix1971
β-strand203114
α-helix204-2085
α-helix216-2183
β-strand229-232415
β-strand243-247515
β-strand250-251216
β-strand255-258416
β-strand266-269416
α-helix270-2723
β-strand273-275315
Chains C and F: 23 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix38-4811
α-helix63-8018
α-helix89-913
α-helix92-10211
α-helix106-1105
α-helix125-1284
α-helix131-14616
α-helix155-1573
α-helix161-1688
α-helix169-1724
α-helix176-19217
α-helix197-20913
α-helix210-2145
α-helix221-23212
α-helix239-2402
α-helix241-2466
α-helix247-2515
α-helix253-2564
α-helix260-2634
α-helix264-27411
α-helix282-29110
α-helix301-31515
α-helix324-3329
Chain E: 15 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix4-118
α-helix15-206
α-helix25-3410
α-helix37-404
β-strand61-71115
β-strand74-83105
β-strand89-9465
α-helix99-11214
β-strand118-12145
α-helix130-1389
β-strand142-14545
α-helix151-1544
α-helix155-17420
α-helix180-18910
α-helix190-1945
α-helix1951
β-strand19616
α-helix1971
β-strand20316
α-helix204-2085
α-helix216-2183
β-strand229-23247
β-strand243-24757
β-strand250-25128
β-strand255-25848
β-strand266-26948
α-helix270-2723
β-strand273-27537

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
IntegraseA, B, D, Eprotein301Simian T-lymphotropic virus 1Q4QY51
PC4 and SFRS1-interacting protein,Serine/threonine-protein phosphatase 2A 56 kDa regulatory…C, Fprotein697Homo sapiensO75475 (AlphaFold model), Q13362 (AlphaFold model)
DNA (5'-d(*ap*cp*tp*gp*tp*gp*tp*tp*tp*gp*gp*cp*gp*cp*tp*tp*cp*tp*cp*tp*c)-3')I, KDNA30Simian T-lymphotropic virus 1
DNA (5'-d(*gp*ap*gp*ap*gp*ap*ap*gp*cp*gp*cp*cp*ap*ap*ap*cp*ap*cp*a)-3')J, LDNA28Simian T-lymphotropic virus 1
Sequence of entity 1 (A, B, D, E), FASTA
>7OUH_1 Integrase (chains A, B, D, E)
GPEFQLSPAKLHSFTHCGQAALTLHGATTTEALNILHSCHACRKNNPQHQMPRGHIRRGL
LPNHIWQGDITHFKYKNTLYRLHVWVDTFSGSVSATHKKRETSSEAISSLLHAIAHLGRP
SHINTDNGPAYASQEFQHACTSLAIRHTTHIPYNPTSSGLVERTNGILKTLLYKYFSDNP
NLPMDNALSVALWTINHLNVLTHCQKTRWQLHHSPRLPPIPEEKPVTTSKTHWYYFKIPG
LNSRQWKGPQRALQEAAGAALIPVSDTAAQWIPWKLLKRAVCPRLAGDTADPKERDHQHH
G
Sequence of entity 2 (C, F), FASTA
>7OUH_2 PC4 and SFRS1-interacting protein,Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform (chains C, F)
SMTRDFKPGDLIFAKMKGYPHWPARVDEVPDGAVKPPTNKLPIFFFGTHETAFLGPKDIF
PYSENKEKYGKPNKRKGFNEGLWEIDNNPKVKFSSQQAATKQSNASSDVEVEEKETSVSK
EDTDHEEKASNEDVTKAVDITTPKAARRGRKRKAEKQVETEEAGVVTTATASVNLKVSPK
RGRPAATEVKIPKPRGRPKMVKQPCPSESDIITEEDKSKKKGQEEKQPKKQPKKDEEGQK
EEDKPRKEPDKKEGKKEVESKRKNLAKTGVTSTSDSEEEGDDQEGEKKRKGGRNFQTAHR
RNMLKGQHEKEAADRKRKQEEQMETEFMVVDAANSNGPFQPVVLLHIRDVPPADQEKLFI
QKLRQCCVLFDFVSDPLSDLKWKEVKRAALSEMVEYITHNRNVITEPIYPEVVHMFAVNM
FRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQLVYEFFLRFLESPDFQPNIAKKYIDQKF
VLQLLELFDSEDPRERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAE
LLEILGSIINGFALPLKEEHKIFLLKVLLPLHKVKSLSVYHPQLAYCVVQFLEKDSTLTE
PVVMALLKYWPKTHSPKEVMFLNELEEILDVIEPSEFVKIMEPLFRQLAKCVSSPHFQVA
ERALYYWNNEYIMSLISDNAAKILPIMFPSLYRNSKT
Sequence of entity 3 (I, K), FASTA
>7OUH_3 DNA (5'-D(*AP*CP*TP*GP*TP*GP*TP*TP*TP*GP*GP*CP*GP*CP*TP*TP*CP*TP*CP*TP*C)-3') (chains I, K)
ACTGTGTTTGGCGCTTCTCTCCCGGAGAGA
Sequence of entity 4 (J, L), FASTA
>7OUH_4 DNA (5'-D(*GP*AP*GP*AP*GP*AP*AP*GP*CP*GP*CP*CP*AP*AP*AP*CP*AP*CP*A)-3') (chains J, L)
TCTCTCCGGGAGAGAAGCGCCAAACACA

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn4
MGMagnesium ionMg4
KLQBictegravirC21 H18 F3 N3 O52

Primary citation

Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures. Barski, M.S., Vanzo, T., Zhao, X.Z. et al. Nat Commun (2021) 12:4996-4996. DOI 10.1038/s41467-021-25284-1 · PubMed

Other PDB entries of the same protein (UniProt Q4QY51), best resolution first:

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