7PEL: Simian T-cell lymphotropic virus intasome

CryoEM structure of simian T-cell lymphotropic virus intasome in complex with PP2A regulatory subunit B56 gamma. Determined by electron microscopy at 3.34 Å resolution. Released 25 Aug 2021.

Method
Electron microscopy
Resolution
3.34 Å
Organisms
Simian T-lymphotropic virus 1, Homo sapiens, synthetic construct
Chains
10
Atoms
14,998
Mol. weight
332.22 kDa
Ligands
ZN
Released
25 Aug 2021

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

Secondary structure: helices and β-sheets

7PEL contains 94 α-helices and 46 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: 14 helices, 13 β-strands

ElementResiduesLengthSheet
α-helix4-118
α-helix15-206
α-helix25-339
β-strand61-70101
β-strand75-8391
β-strand89-9461
α-helix99-11315
β-strand118-12251
α-helix130-1378
β-strand142-14651
α-helix159-17416
α-helix181-1899
α-helix190-1945
α-helix1951
β-strand19612
α-helix1971
β-strand20312
α-helix204-2096
α-helix211-2155
α-helix223-2286
β-strand229-23243
β-strand245-24733
β-strand251-25224
β-strand255-25844
β-strand266-26834
α-helix270-2723
β-strand273-27533
Chains B and E: 13 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix4-118
α-helix15-184
α-helix19-213
α-helix25-3410
α-helix36-394
α-helix48-503
β-strand61-71115
β-strand74-83105
β-strand89-9465
α-helix99-11315
β-strand118-12145
α-helix130-1389
β-strand142-14545
α-helix155-17420
α-helix180-18910
α-helix190-1945
α-helix204-2085
α-helix216-2183
β-strand229-23246
β-strand243-24756
β-strand255-25847
β-strand266-26947
β-strand273-27536
Chains C and F: 20 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix38-4710
α-helix63-7917
α-helix89-913
α-helix92-10211
α-helix106-1105
α-helix131-14515
α-helix161-1688
α-helix176-19217
α-helix197-20913
α-helix210-2145
α-helix223-23210
α-helix239-2402
α-helix241-2466
α-helix247-2515
α-helix252-2565
α-helix258-2636
α-helix264-27411
α-helix283-2897
α-helix301-31515
α-helix324-3329

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Pol proteinA, B, D, Eprotein301Simian T-lymphotropic virus 1Q4QY51
Isoform 3 of PC4 and SFRS1-interacting protein,Isoform Gamma-2 of Serine/threonine-protein…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')K, MDNA30synthetic construct
DNA (5'-d(*gp*ap*gp*ap*gp*ap*ap*gp*cp*gp*cp*cp*ap*ap*ap*cp*ap*cp*a)-3')L, NDNA28synthetic construct
Sequence of entity 1 (A, B, D, E), FASTA
>7PEL_1 Pol protein (chains A, B, D, E)
GPEFQLSPAKLHSFTHCGQAALTLHGATTTEALNILHSCHACRKNNPQHQMPRGHIRRGL
LPNHIWQGDITHFKYKNTLYRLHVWVDTFSGSVSATHKKRETSSEAISSLLHAIAHLGRP
SHINTDNGPAYASQEFQHACTSLAIRHTTHIPYNPTSSGLVERTNGILKTLLYKYFSDNP
NLPMDNALSVALWTINHLNVLTHCQKTRWQLHHSPRLPPIPEAKPVTTSKTHWYYFKIPG
LNSRQWKGPQRALQEAAGAALIPVSDTAAQWIPWKLLKRAVCPRLAGDTADPKERDHQHH
G
Sequence of entity 2 (C, F), FASTA
>7PEL_2 Isoform 3 of PC4 and SFRS1-interacting protein,Isoform Gamma-2 of 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 (K, M), FASTA
>7PEL_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 K, M)
ACTGTGTTTGGCGCTTCTCTCCCGGAGAGA
Sequence of entity 4 (L, N), FASTA
>7PEL_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 L, N)
TCTCTCCGGGAGAGAAGCGCCAAACACA

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn4

Primary citation

Cryo-EM structure of the deltaretroviral intasome in complex with the PP2A regulatory subunit B56gamma. Barski, M.S., Minnell, J.J., Hodakova, Z. et al. Nat Commun (2020) 11:5043. DOI 10.1038/s41467-020-18874-y · PubMed

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

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