Structure of tetrameric HIV-1 Strand Transfer Complex Intasome

2024-03-13 REL RCSB RCSB RCSB 2016-11-28 2017-01-11 2017-01-11 2024-03-13 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM103368 United States Leona M. and Harry B. Helmsley Charitble Trust Grant #2012-PG-MED002 United States National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) Intramural Program of the National Institute of Diabetes and Digestive Diseases United States Structure of tetrameric HIV-1 Strand Transfer Complex Intasome Lyumkis D Passos D integrase, integration, transposase, transesterification, VIRAL PROTEIN Passos DO Li M Yang R Rebensburg SV Ghirlando R Jeon Y Shkriabai N Kvaratskhelia M Craigie R Lyumkis D Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. Science US 355 89 92 2017 28059769 doi:10.1126/science.aah5163 1095-9203 0038 SCIEAS EMD-8483 other EM volume 5u1c FULLOVERLAP complex formed by a tetrameric assembly of Sso7d-fusion HIV-1 Integrase with the product of DNA strand transfer complex formed by a tetrameric assembly of Sso7d-fusion HIV-1 Integrase with the product of DNA strand transfer 0 1 2 3 4 Human immunodeficiency virus 1 0.228 HIV-1 Integrase, Sso7d chimera Human immunodeficiency virus 1 0.042320273 4 Escherichia coli LEVO MGSSHHHHHHSSGLVPRGSHMATVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLE KQKKGGGGGGGGGGGFLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDC THLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNP QSQGVIQSMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRV YYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED A0A157T5S7 F2WR39 DNA (11-MER) Homo sapiens 0.003349197 2 (DG)(DT)(DA)(DC)(DG)(DC)(DT)(DG)(DA)(DC)(DT) DNA DNA (23-MER) Human immunodeficiency virus 1 0.007015546 2 (DA)(DC)(DT)(DG)(DC)(DT)(DA)(DG)(DA)(DG)(DA)(DT)(DT)(DT)(DT)(DC)(DC)(DA)(DC)(DA) (DC)(DT)(DG) DNA DNA (37-MER) Homo sapiens 0.011414358 2 (DC)(DA)(DG)(DT)(DG)(DT)(DG)(DG)(DA)(DA)(DA)(DA)(DT)(DC)(DT)(DC)(DT)(DA)(DG)(DC) (DA)(DG)(DT)(DT)(DA)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DC)(DG)(DT)(DA)(DC) DNA ZINC ION 6.5409e-05 2 ZN MAGNESIUM ION 2.4305e-05 2 MG singleParticle particle 0.5 8.0 500.0 NaCl sodium chloride 20.0 C4H11NO3 Tris 0.5 C9H15O6P TCEP 6.0 C3H8O3 glycerol Quantifoil GOLD 400 PLASMA CLEANING 6 OTHER ETHANE 50 277 HOMEMADE PLUNGER

Sample containing HIV STC intasomes in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey gold UltrAuFoil grids (Quantifoil), adsorbed for 30 seconds, then plunged into liquid ethane using a manual cryo-plunger in an ambient environment of 4 degrees C..

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.5 4.0 22500.0 38167.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 90.0 90.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1-100 1 1225 20.0 95.0

Individual frames were gain-corrected, aligned, and summed with the application of an exposure filter using MotionCor2, according to the nominal dose rate.

1 274764 common lines model using OptiMod

An initial model was generated directly from the class averages using OptiMod.

C2 FOURIER SPACE 3.9 FSC 0.143 CUT-OFF FREALIGN 9.11

Resolution-limited refinement used throughout

83766 PROJECTION MATCHING 7.5 RELION 1.3

Relion 3D classification, auto mode

PROJECTION MATCHING FREALIGN 9.11

Frealign 3D classification and refinement

FREALIGN 3.11 emd_8481.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 251.51999 251.51999 251.51999 90.0 90.0 90.0 X Y Z -0.188862 0.36068627 0.00052015175 0.011994169 1.31 1.31 1.31 0.08 AUTHOR ::::EMDATABANK.org::::EMD-8481:::: cryoEM reconstruction of a tetrameric HIV-1 strand transfer complex intasome FLEXIBLE FIT

To generate ensemble models, the complete intasome model was iteratively relaxed - using two-fold symmetry and a combination of Rosetta and Phenix - against one half map (the working map) and inspected for consistency with the second half map (the free map). The model was then adjusted manually using Coot. Final ensemble modeling used half maps for all aspects of refinement and evaluation: 500 models were generated as described using Rosetta. From the 100 top-scoring models (scored by Rosetta energy), the ten models with the best map-to-model FSC were selected and refined in real space using secondary-structure restraints in Phenix. Molprobity was used throughout the refinement process.

FSC 0.5 REAL 180.0 emd_8481_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 251.51999 251.51999 251.51999 90.0 90.0 90.0 X Y Z -0.13385755 0.39770308 0.0024832604 0.016528426 1.31 1.31 1.31 AUTHOR ::::EMDATABANK.org::::EMD-8481:::: cryoEM reconstruction of a tetrameric HIV-1 strand transfer complex intasome, map 1 emd_8481_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 251.51999 251.51999 251.51999 90.0 90.0 90.0 X Y Z -0.1330024 0.39115524 0.002575401 0.016512973 1.31 1.31 1.31 AUTHOR ::::EMDATABANK.org::::EMD-8481:::: cryoEM reconstruction of a tetrameric HIV-1 strand transfer complex intasome, map 2