2021-08-25 OBS PDBe PDBe PDBe 2020-05-18 2020-10-21 2020-10-21 2021-08-25 2021-08-25 Wellcome Trust 107005/Z/15Z United Kingdom Royal Society RG120032 United Kingdom Cancer Research UK FC001061 United Kingdom Medical Research Council (MRC, United Kingdom) FC001061 United Kingdom Wellcome Trust FC001061 United Kingdom CryoEM structure of simian T-cell lymphotropic virus intasome in complex with PP2A regulatory subunit B56 gamma Barski M Hodakova Z Nans A Cherepanov P Maertens GN Barski MS Minnell JJ Hodakova Z Pye VE Nans A Cherepanov P Maertens GN Cryo-EM structure of the deltaretroviral intasome in complex with the PP2A regulatory subunit B56 gamma. Nat Commun UK 11 5043 5043 2020 33028863 doi:10.1038/s41467-020-18874-y 2041-1723 EMD-11052 associated EM volume
CryoEM structure of simian T-cell lymphotropic virus intasome in complex with PP2A regulatory subunit B56 gamma
 6z2y FULLOVERLAP Complex of STLV-1 MarB43 integrase with nascent viral DNA and the human PP2A B56 subunit Complex of STLV-1 MarB43 integrase with nascent viral DNA and the human PP2A B56 subunit 0 1 2 3 4
Sample composition and source have been described in "macromolecules"
 Pol Protein 1 1
Pol Protein
Simian T-lymphotropic virus 1 Escherichia coli PC4 and SFRS1-interacting protein,Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform 1 2
PC4 and SFRS1-interacting protein,Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
Homo sapiens Escherichia coli DNA 1 3 4
DNA
Simian T-lymphotropic virus 1 synthetic construct Pol protein Simian T-lymphotropic virus 1 0.033885504 4 Escherichia coli LEVO GPEFQLSPAKLHSFTHCGQAALTLHGATTTEALNILHSCHACRKNNPQHQMPRGHIRRGLLPNHIWQGDITHFKYKNTLY RLHVWVDTFSGSVSATHKKRETSSEAISSLLHAIAHLGRPSHINTDNGPAYASQEFQHACTSLAIRHTTHIPYNPTSSGL VERTNGILKTLLYKYFSDNPNLPMDNALSVALWTINHLNVLTHCQKTRWQLHHSPRLPPIPEAKPVTTSKTHWYYFKIPG LNSRQWKGPQRALQEAAGAALIPVSDTAAQWIPWKLLKRAVCPRLAGDTADPKERDHQHHG PC4 and SFRS1-interacting protein,Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform Homo sapiens 0.08039468
fusion construct containing human LEDGF (residues 1-324 thus without the IBD domain) (gene PSIP1; O75475)) and human B56gammma (residues 11-380) regulatory subunit of PP2A (gene PPP2R5C) (no space for these details below),fusion construct containing human LEDGF (residues 1-324 thus without the IBD domain) (gene PSIP1; O75475)) and human B56gammma (residues 11-380) regulatory subunit of PP2A (gene PPP2R5C) (no space for these details below)
2 Escherichia coli LEVO SMTRDFKPGDLIFAKMKGYPHWPARVDEVPDGAVKPPTNKLPIFFFGTHETAFLGPKDIFPYSENKEKYGKPNKRKGFNE GLWEIDNNPKVKFSSQQAATKQSNASSDVEVEEKETSVSKEDTDHEEKASNEDVTKAVDITTPKAARRGRKRKAEKQVET EEAGVVTTATASVNLKVSPKRGRPAATEVKIPKPRGRPKMVKQPCPSESDIITEEDKSKKKGQEEKQPKKQPKKDEEGQK EEDKPRKEPDKKEGKKEVESKRKNLAKTGVTSTSDSEEEGDDQEGEKKRKGGRNFQTAHRRNMLKGQHEKEAADRKRKQE EQMETEFMVVDAANSNGPFQPVVLLHIRDVPPADQEKLFIQKLRQCCVLFDFVSDPLSDLKWKEVKRAALSEMVEYITHN RNVITEPIYPEVVHMFAVNMFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQLVYEFFLRFLESPDFQPNIAKKYIDQKF VLQLLELFDSEDPRERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSIINGFALPLKEEH KIFLLKVLLPLHKVKSLSVYHPQLAYCVVQFLEKDSTLTEPVVMALLKYWPKTHSPKEVMFLNELEEILDVIEPSEFVKI MEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDNAAKILPIMFPSLYRNSKT 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') Simian T-lymphotropic virus 1 0.009221908999999999 2 (DA)(DC)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DG)(DG)(DC)(DG)(DC)(DT)(DT)(DC)(DT)(DC)(DT) (DC)(DC)(DC)(DG)(DG)(DA)(DG)(DA)(DG)(DA) DNA DNA (5'-D(*GP*AP*GP*AP*GP*AP*AP*GP*CP*GP*CP*CP*AP*AP*AP*CP*AP*CP*A)-3') Simian T-lymphotropic virus 1 0.008593559999999998 2 (DT)(DC)(DT)(DC)(DT)(DC)(DC)(DG)(DG)(DG)(DA)(DG)(DA)(DG)(DA)(DA)(DG)(DC)(DG)(DC) (DC)(DA)(DA)(DA)(DC)(DA)(DC)(DA) DNA ZINC ION 6.5409e-05 4 ZN singleParticle particle 0.76 6.0 20.0 Bis tris propane 0.3 NaCl Sodium Chloride C-flat-1.2/1.3 GOLD CARBON HOLEY 20.0 ETHANE 95 295.15 FEI VITROBOT MARK IV
Complex has been purified by SEC chromatography
 6.0 20.0 Bis tris propane 0.3 NaCl Sodium Chloride C-flat-1.2/1.3 GOLD CARBON HOLEY 20.0 ETHANE 95 295.15 FEI VITROBOT MARK IV
Complex has been purified by SEC chromatography
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 FEI FALCON III (4k x 4k) COUNTING 50.4 1 4356108
2,198,454 (OH dataset) and 2,157,654 (GO dataset) 3D reconstructions using either separate subsets resulted in highly anisotropic maps due to severe preferential orientations. Because 3D-FCS analysis indicated favourable complementarity of the data, the datasets were merged as separate optic groups in Relion-3.1. 3D reconstruction, including Bayesian particle polishing, CTF and beam tilt refinement, as implemented in Relion-3.1, resulted in the final map with minimal anisotropy; 3D-FSC sphericity index of the final map was 0.967.
 Gctf 1.06
ab initio mask made in crysparc
 C2 3.34 FSC 0.143 CUT-OFF RELION 3.1
3D reconstruction, including Bayesian particle polishing, CTF and beam tilt refinement, as implemented in Relion-3.1, resulted in the final map with minimal anisotropy; 3D-FSC sphericity index of the final map was 0.967.
161921 PROJECTION MATCHING cryoSPARC 2 PROJECTION MATCHING cryoSPARC 3.1 17 35276.0 RELION 3.1
After reference free 2D classification in CryoSPARC-2 those particles belonging to well-defined classes (599,700 and 493,665 particles for OH and GO datasets, respectively) were subjected to 45 cycles of 3D classification into 17 (OH) or 13 (GO) classes in Relion-3.0 without imposing symmetry. The procedure yielded a single high-resolution class from each dataset. Particles belonging to the best 3D classes (94,517 and 67,404 from OH and GO dataset, respectively) were re-extracted as full-sized images. 3D reconstructions using either separate subsets resulted in highly anisotropic maps due to severe preferential orientations. Because 3D-FCS analysis indicated favourable complementarity of the data, the datasets were merged as separate optic groups in Relion-3.1.
 emd_11052.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 76 137 113 110 82 94 113 137 76 123.170006 149.33 82.840004 90.0 90.0 90.0 Z Y X -2.466581 3.8886082 -7.282095e-14 0.24949118 1.09 1.09 1.09 0.15 AUTHOR Density Modified map generated using Resolve in Phenix. Contour 0.15, step 1 in Chimera; 3 rmsd in Coot 6QBW A 53-221 6TOQ A 212-218 6TJU C 238-286 5JJA A 29-375 RIGID BODY FIT REAL 31.31 AB INITIO MODEL
Baverage protein=31.31; DNA=49.12; zinc=38.96
REAL 31.31 emd_11052_msk_1.map emd_11052_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 327.0 327.0 327.0 90.0 90.0 90.0 X Y Z -0.025976144 0.09308051 0.00027863757 0.0027955505 1.09 1.09 1.09 AUTHOR original half map 2 emd_11052_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 327.0 327.0 327.0 90.0 90.0 90.0 X Y Z -0.15741798 0.2916577 0.0001350498 0.007915029 1.09 1.09 1.09 AUTHOR Map autosharpened in Relion, B= -143, Contour 0.03, step 1 in Chimera; 8.7 rmsd in coot emd_11052_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 327.0 327.0 327.0 90.0 90.0 90.0 X Y Z -0.025384616 0.09552373 -8.537963e-06 0.0028035378 1.09 1.09 1.09 AUTHOR original half map 1